apbs-users — Moderate-traffic APBS user discussion list

[apbs-users] Variable dielectric inside the protein - is there a way for APBS to take into account?

[Boaz S. <bsh...@bg...>]

Dear Nathan and list,

With chimerax, it is now possible to visualize the electrostatic potential inside a protein (e.g. around a binding site) which is wonderful.
In the calculation of the electrostatic potential (.dx) we assume that the internal dielectric potential inside is 2 and constant, and lower than the solvent dielectric constant (80). I've seen articles dealing with the variability of the internal dielectric depending on the local environment but it seems as there is no consensus, obviously because there is no simple answer. Even so, I'm wondering whether there is way to deal with this issue somehow, even in an approximate way in APBS.

I'd appreciate any input.

Best wishes,

             Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bsh...@bg...
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710

[apbs-users] This mailing list is shutting down

[Baker, N. <nat...@pn...>]

Hi All –

This mailing list is shutting down.  Please use https://github.com/Electrostatics/apbs/issues for issues related to APBS support.

Thank you,

--
Nathan Baker
http://pronoun.is/he
Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
https://www.linkedin.com/in/nathanandrewbaker/

[apbs-users] writemat

[Ema S. <ema...@ki...>]

Hello.

While running APBS I want to obtain map of Poisson operator. When i run 
the program, it writes on the screen: Writing Poisson operator matrix to 
poissom_21.9.mat..., but file can not be found. We also tried in on a 
DNA tutorial input file. Could you tell me if there is a bug in the 
code, or is it suppose to work normally and I have a mistake in an input 
file. Please find my input file in attachment.

Best regards

Ema Slejko

Re: [apbs-users] APBS vs UHBD potentials

[Nathan B. <nat...@gm...>]

Hello -

I notice that you have pre-calculated grids in your UHBD calculation; where did you get those grids?  What surface definition did you use?

It also appears that you are using cubic splines in APBS for the charge discretization; I think that UHBD only used trilinear (but don't remember exactly).  One of the things we tried to avoid with APBS was default parameter settings:  all of the parameters and their settings must be specified in the input file.  Can you either specify the settings for the inputs in UHBD and/or send me a copy of the output?

Unfortunately, SF.net restricts the size of message to the mailing list.  That is one of the reasons why https://github.com/Electrostatics/apbs/issues is our preferred channel for support.

Thank you,

Nathan Baker

From: Murga, Leonel <l....@no...>
Sent: 13 August, 2020 15:36
To: apb...@li...
Subject: [apbs-users] APBS vs UHBD potentials

Hello,

I am in the process of migrating our calculations from UHBD to APBS. As part of this process I am trying to understand what settings I need to use in APBS to reproduce our results in UHBD.

The goal is to calculate the electrostatic potential produced by a single +1 charge placed in some particular positions in a test structure at all the other positions in the same structure. Files pkaSH.pqr is the original structure and file pkaSH_Mod.pqr had all the charges set to zero except the first one that is set to 1. The calculation was done both in APBS and UHBD (the input files are attached). Values of the electrostatic potentials were calculated using the multivalue utility that comes with APBS at the coordinates of interest (pkaSH.csv) and were converted to (kcal mol-1 e-1) to compare to the output produced by UHBD.  Quite a few values were different between the two. I reproduce some here:

                                    X           Y           Z              Q             PHI UHBD (kcal/mol)/e       PHI APBS kT/e        PHI APBS (kcal/mol)/e     % Diff
  1n       ala     1      22.402    10.3   7.094        -0.3                 4.11E+01                       6.49E+01                     3.78E+01                           8.0
111o    asn    13      6.195   18.081  11.358    -0.55               3.39E-02                        6.54E-02                      3.81E-02                          12.1
216ca   gly     26    33.341  10.398  23.256     0.1                  2.53E-02                        5.03E-02                      2.93E-02                          15.8
219h     gly     26    33.45    12.523  23.003     0.25               2.44E-02                         4.89E-02                     2.85E-02                           16.6

The average error was 5.8%.

Could you please help me understand why some of the values are so different between APBS and UHBD? Is there anything I should do to increase the similarity between the two outputs? Thanks!

Best,

Leonel Murga
Northeastern University
Chemistry Department

P.S.: Could you please increase the size of the allowed messages to the list? 100 kB does not allow for much to be attached.

Re: [apbs-users] APBS vs UHBD potentials

[Murga, L. <l....@no...>]

Hello,

One more thing. I realized after sending the previous message that the APBS input file that I attached has the parameter sdens set to 500. The calculation in the previous message was really done with sdens 10 (default value). I ran a few other tests with different values of sdens -the last one being sdens 500- but I obtained about the same results. Apologies for any confusion.

And, since I am sending this message I am also attaching the full comparison of the potentials between UHBD and APBS. Thanks

Best,

Leonel Murga
Northeastern University
Chemistry Department
________________________________
From: Murga, Leonel <l....@no...>
Sent: Thursday, August 13, 2020 6:35 PM
To: apb...@li... <apb...@li...>
Subject: [apbs-users] APBS vs UHBD potentials

Hello,

I am in the process of migrating our calculations from UHBD to APBS. As part of this process I am trying to understand what settings I need to use in APBS to reproduce our results in UHBD.

The goal is to calculate the electrostatic potential produced by a single +1 charge placed in some particular positions in a test structure at all the other positions in the same structure. Files pkaSH.pqr is the original structure and file pkaSH_Mod.pqr had all the charges set to zero except the first one that is set to 1. The calculation was done both in APBS and UHBD (the input files are attached). Values of the electrostatic potentials were calculated using the multivalue utility that comes with APBS at the coordinates of interest (pkaSH.csv) and were converted to (kcal mol-1 e-1) to compare to the output produced by UHBD.  Quite a few values were different between the two. I reproduce some here:

                                    X           Y           Z              Q             PHI UHBD (kcal/mol)/e       PHI APBS kT/e        PHI APBS (kcal/mol)/e     % Diff
  1n       ala     1      22.402    10.3   7.094        -0.3                 4.11E+01                       6.49E+01                     3.78E+01                           8.0
111o    asn    13      6.195   18.081  11.358    -0.55               3.39E-02                        6.54E-02                      3.81E-02                          12.1
216ca   gly     26    33.341  10.398  23.256     0.1                  2.53E-02                        5.03E-02                      2.93E-02                          15.8
219h     gly     26    33.45    12.523  23.003     0.25               2.44E-02                         4.89E-02                     2.85E-02                           16.6

The average error was 5.8%.

Could you please help me understand why some of the values are so different between APBS and UHBD? Is there anything I should do to increase the similarity between the two outputs? Thanks!

Best,

Leonel Murga
Northeastern University
Chemistry Department

P.S.: Could you please increase the size of the allowed messages to the list? 100 kB does not allow for much to be attached.

[apbs-users] APBS vs UHBD potentials

[Murga, L. <l....@no...>]

Hello,

I am in the process of migrating our calculations from UHBD to APBS. As part of this process I am trying to understand what settings I need to use in APBS to reproduce our results in UHBD.

The goal is to calculate the electrostatic potential produced by a single +1 charge placed in some particular positions in a test structure at all the other positions in the same structure. Files pkaSH.pqr is the original structure and file pkaSH_Mod.pqr had all the charges set to zero except the first one that is set to 1. The calculation was done both in APBS and UHBD (the input files are attached). Values of the electrostatic potentials were calculated using the multivalue utility that comes with APBS at the coordinates of interest (pkaSH.csv) and were converted to (kcal mol-1 e-1) to compare to the output produced by UHBD.  Quite a few values were different between the two. I reproduce some here:

                                    X           Y           Z              Q             PHI UHBD (kcal/mol)/e       PHI APBS kT/e        PHI APBS (kcal/mol)/e     % Diff
  1n       ala     1      22.402    10.3   7.094        -0.3                 4.11E+01                       6.49E+01                     3.78E+01                           8.0
111o    asn    13      6.195   18.081  11.358    -0.55               3.39E-02                        6.54E-02                      3.81E-02                          12.1
216ca   gly     26    33.341  10.398  23.256     0.1                  2.53E-02                        5.03E-02                      2.93E-02                          15.8
219h     gly     26    33.45    12.523  23.003     0.25               2.44E-02                         4.89E-02                     2.85E-02                           16.6

The average error was 5.8%.

Could you please help me understand why some of the values are so different between APBS and UHBD? Is there anything I should do to increase the similarity between the two outputs? Thanks!

Best,

Leonel Murga
Northeastern University
Chemistry Department

P.S.: Could you please increase the size of the allowed messages to the list? 100 kB does not allow for much to be attached.

[apbs-users] dielectric maps

[Ema S. <ema...@ki...>]

Hello.

I have faced some problems with running APBS, with dielectric maps as an 
input. To properly run the APBS, I also created kappa map, as suggested 
in APBS documentation. I obtained no difference between different APBS 
runs, with different dielectric maps. However output dielectric maps and 
kappa map are different from those I use as an input. So I am guessing 
APBS does not read my diel maps and kappa map. I put the maps in the 
read section as it is said in documentation. Is there anything else I 
should change, so diel maps and kappa map will be read?

Best regards

Ema Slejko

Re: [apbs-users] dielectric maps

[Frank M. <fvm...@gm...>]

Hi Ema,

The dielectric maps dielx, diely and dielz are the dielectric at locations
shifted half of a grid spacing in x, y, and z respectively relative to the
input charge density map (charge) and output potential map (phi). If
charge[i, j, k] is the charge density at location (x[i], y[j], z[k]), then
diely[i, j, k] is the dielectric at location (x[i], (y[j]+y[j+1])/2, z[k]),
where i, j and k run from 1 to the grid dimension in x, y, and z,
respectively.

The dielectric maps are shifted relative to the other grids to make
evaluation of the dielectric energy density simple. The dielectric energy
density is u = epsilon (grad phi)^2 / 2. To evaluate this using the lowest
order finite difference approximation, the following expression is used by
APBS:
u[i,j,k] = dielx[i,j,k] * (phi[i+1,j,k]-phi[i,j,k])^2 / hx^2 + diely[i,j,k]
* (phi[i,j+1,k]-phi[i,j,k])^2 / hy^2 + dielz[i,j,k] *
(phi[i,j,k+1]-phi[i,j,k])^2 / hz^2, where u is the energy density, phi is
the solution for the electrostatic potential, and hx, hy and hz are the x,
y and z grid spacings, respectively. The total dielectric energy (the
integral of the dielectric energy density) is the sum over i, j and k of hx
* hy * hz * u[i,j,k].

By shifting the dielectric, the gradient of the potential and the
dielectric are both effectively evaluated at the same location.

Kind regards,
Frank





On Mon, Aug 10, 2020 at 9:41 PM Ema Slejko <ema...@ki...> wrote:

> Hello.
>
> I would like to create a dielectric input file. However I do not
> understand how to create three different dielectric maps for x,y,z
> coordinates. For each one we have a same 3D grid but need different
> values. Could you explain me how to calculate values for three input
> files. For now i am working on simple example with two different
> dielectric (for interior of biomolecule and outside of it), but later i
> would like to incorporate data of dielectric constant changed at
> different distances from center of biomolecule.
>
>
> Thank you very much for you help.
>
> Best regards
>
> Ema Slejko
>
> PhD student at Chemistry Institute
>
> Ljubljana Slovenia
>
>
>
> _______________________________________________
> apbs-users mailing list
> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users
>

[apbs-users] dielectric maps

[Ema S. <ema...@ki...>]

Hello.

I would like to create a dielectric input file. However I do not 
understand how to create three different dielectric maps for x,y,z 
coordinates. For each one we have a same 3D grid but need different 
values. Could you explain me how to calculate values for three input 
files. For now i am working on simple example with two different 
dielectric (for interior of biomolecule and outside of it), but later i 
would like to incorporate data of dielectric constant changed at 
different distances from center of biomolecule.


Thank you very much for you help.

Best regards

Ema Slejko

PhD student at Chemistry Institute

Ljubljana Slovenia

Re: [apbs-users] Solvent accessibility

[Baker, N. <nat...@pn...>]

Hello --

Can you please provide an example PQR file so we can attempt to reproduce the problem?

Thank you,



--

Nathan Baker
http://pronoun.is/he

Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
https://www.linkedin.com/in/nathanandrewbaker/

________________________________
From: Amaury Coste <ama...@ki...>
Sent: Monday, July 20, 2020 07:10
To: apb...@li... <apb...@li...>
Subject: [apbs-users] Solvent accessibility


Hello,


I am calculating density profiles of mobile ions and I highlight an issue. The ion accessibility is not set to 0 within the DNA put below the parameters and the output of the solvent accessibility around DNA molecule. Is it something wrong in my parameters or is it a problem of the code.

Thank you very much for your help.

Best regards,


Dr. Amaury Coste



read

mol pqr dna.pqr

end

elec name polar

mg-auto

dime 97 97 161

cglen 160 160 34

fglen 130 130 34

cgcent mol 1

fgcent mol 1

mol 1

lpbe

bcfl zero

pdie 1.0 #2

sdie 78.54 #75.5

ion charge 1.0 conc 0.15 radius 2 #

ion charge -1.0 conc 0.15 radius 2

srfm mol

chgm spl2

sdens 10.00

gamma 0.105

srad 0

swin 0.30

temp 298.15

calcenergy total #calculated apolar energy

calcforce no

write pot dx pot

write qdens dx qdens

write ndens dx ndens

write vdw flat vdw

end

quit





# Data from 1.4

#

# SOLVENT ACCESSIBILITY -- VAN DER WAALS

#

1.000000e+00

1.000000e+00

1.000000e+00

1.000000e+00

etc...

[apbs-users] Solvent accessibility

[Amaury C. <ama...@ki...>]

Hello,


I am calculating density profiles of mobile ions and I highlight an 
issue. The ion accessibility is not set to 0 within the DNA put below 
the parameters and the output of the solvent accessibility around DNA 
molecule. Is it something wrong in my parameters or is it a problem of 
the code.

Thank you very much for your help.

Best regards,


Dr. Amaury Coste



read

mol pqr dna.pqr

end

elec name polar

mg-auto

dime 97 97 161

cglen 160 160 34

fglen 130 130 34

cgcent mol 1

fgcent mol 1

mol 1

lpbe

bcfl zero

pdie 1.0 #2

sdie 78.54 #75.5

ion charge 1.0 conc 0.15 radius 2 #

ion charge -1.0 conc 0.15 radius 2

srfm mol

chgm spl2

sdens 10.00

gamma 0.105

srad 0

swin 0.30

temp 298.15

calcenergy total #calculated apolar energy

calcforce no

write pot dx pot

write qdens dx qdens

write ndens dx ndens

write vdw flat vdw

end

quit





# Data from 1.4

#

# SOLVENT ACCESSIBILITY -- VAN DER WAALS

#

1.000000e+00

1.000000e+00

1.000000e+00

1.000000e+00

etc...

Re: [apbs-users] Problems in Compilation of APBS 3.0

[Robert K. <ro...@uc...>]

Hi Leo,

I think some components of APBS 3.0 need a newer version of gcc than what 
is installed by default on Centos 7 (4.8.5). You can install gcc version 7, 
for example, via SCL:

yum install centos-release-scl
yum install devtoolset-7

Then his worked for me, on Centos 7.7:

scl enable devtoolset-7 bash
cmake3 .. \
  -DGET_MSMS=ON \
  -DGET_NanoShaper=ON \
  -DCMAKE_BUILD_TYPE=Release          \
  -DENABLE_GEOFLOW=ON                 \
  -DENABLE_BEM=ON                     \
  -DENABLE_FETK=ON                    \
  -DENABLE_OPENMP=ON                  \
  -DENABLE_PBAM=ON                    \
  -DENABLE_PBSAM=ON                   \
  -DENABLE_PYTHON=ON                  \
  -DBUILD_SHARED_LIBS=ON \
  -DCMAKE_C_FLAGS="-fPIC" \
  -DENABLE_TESTS=ON                   \
  -DBUILD_DOC=ON                     \
  -DCMAKE_INSTALL_PREFIX=/opt/apbs-3.0.0

make && make install


Best,

Robert

On Wed, Jul 08, 2020 at 07:59:17PM +0000, Murga, Leonel wrote:
>   Hello,
>   We are trying to compile APBS 3.0 under Centos 7 using cmake 3.17. The
>   process simply dies with a message that does not tell me much about
>   what is happening.
>   This is what we did:
>   1) Downloaded the source code for Linux
>   2) Expanded the tgz file
>   3) Went into the apbs directory
>   4) Tried to compile with cmake path_to_apbs_directory
>   At this point the process dies with a message "Configuring incomplete,
>   errors occurred!"
>   We did the compilation again using the verbose mode for cmake to see if
>   I obtained more information. Something that we noticed is that we get
>   the following error in the cmake output:
>   CMake Error at CMakeLists.txt:310 (add_subdirectory):
>     add_subdirectory given source
>     "/home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/externals/fetk/maloc"
>   which is
>     not an existing directory.
>   There is a fetk directory in the apbs tree but it is empty which maybe
>   explains the error.
>   Do we need to download additional files? If so, from where.
>   Are all the options like FETK, PB-AM, etc. activated by default?
>   Please advise. Thanks for your help
>   Leo
>   Attached you will find the the output of the cmake command and the
>   CMakeOutput.log

>CMake Deprecation Warning at CMakeLists.txt:10 (cmake_policy):
>  The OLD behavior for policy CMP0054 will be removed from a future version
>  of CMake.
>
>  The cmake-policies(7) manual explains that the OLD behaviors of all
>  policies are deprecated and that a policy should be set to OLD only under
>  specific short-term circumstances.  Projects should be ported to the NEW
>  behavior and not rely on setting a policy to OLD.
>
>
>-- Setting project paths
>-- Setting lookup paths for headers and libraries
>-- Computing machine epsilon values
>-- Floating point epsilon is 2.220446e-16
>-- Double precision epsilon is 2.220446e-16
>CMake Error at CMakeLists.txt:310 (add_subdirectory):
>  add_subdirectory given source
>  "/home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/externals/fetk/maloc" which is
>  not an existing directory.
>
>
>-- Inline functions enabled
>-- Verbose debugging mode enabled
>-- Adding apbs_generic
>-- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c
>-- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h
>-- With internal header files
>-- With library dependencies m;stdc++;maloc
>-- Added apbs_generic
>-- Adding apbs_pmgc
>-- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c
>-- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h
>-- With internal header files
>-- With library dependencies m;stdc++;maloc
>-- Added apbs_pmgc
>-- Adding apbs_mg
>-- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c
>-- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h
>-- With internal header files
>-- With library dependencies m;stdc++;maloc;apbs_generic;apbs_pmgc
>-- Added apbs_mg
>-- Adding apbs_routines
>-- With source files routines.c
>-- With external header files
>-- With internal header files
>-- With library dependencies m;stdc++;maloc
>-- Added apbs_routines
>-- External Headers:
>--
>-- APBS Libraries: m;stdc++;maloc
>-- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines
>--
>--  -fPIC
>-- Supplemental tools enabled
>-- Building mesh
>-- libraries: apbs_generic;apbs_mg;apbs_pmgc
>-- Building manip
>-- libraries: apbs_generic;apbs_mg;apbs_pmgc
>-- ******* Python3 FOUND /usr/local/bin/python3.7
>-- TEST born_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t born
>-- TEST actin-dimer-auto_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t actin-dimer-auto
>-- TEST actin-dimer-parallel_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t actin-dimer-parallel
>-- TEST alkanes_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t alkanes
>-- TEST FKBP_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t FKBP
>-- TEST hca-bind_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t hca-bind
>-- TEST ionize_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t ionize
>-- TEST ion-pmf_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t ion-pmf
>-- TEST ion-protein_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t ion-protein
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>-- TEST geoflow_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t geoflow
>-- TEST bem_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t bem
>-- TEST bem-pKa_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t bem-pKa
>-- TEST bem-binding-energy_test COMMAND /usr/local/bin/python3.7 /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/apbs_tester.py -c /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/tests/test_cases.cfg -e /home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/apbs -t bem-binding-energy
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>


>_______________________________________________
>apbs-users mailing list
>apb...@li...
>https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/apbs-users__;!!Mih3wA!TClPTxbeqzX6X2x14O_JrZq4KpTFi-amiHQ6N5gfSCBPJdds3NStWEfl45PX$

[apbs-users] Problems in Compilation of APBS 3.0

[Murga, L. <l....@no...>]

Hello,

We are trying to compile APBS 3.0 under Centos 7 using cmake 3.17. The process simply dies with a message that does not tell me much about what is happening.

This is what we did:
1) Downloaded the source code for Linux
2) Expanded the tgz file
3) Went into the apbs directory
4) Tried to compile with cmake path_to_apbs_directory

At this point the process dies with a message "Configuring incomplete, errors occurred!"

We did the compilation again using the verbose mode for cmake to see if I obtained more information. Something that we noticed is that we get the following error in the cmake output:

CMake Error at CMakeLists.txt:310 (add_subdirectory):
  add_subdirectory given source
  "/home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/externals/fetk/maloc" which is
  not an existing directory.

There is a fetk directory in the apbs tree but it is empty which maybe explains the error.

Do we need to download additional files? If so, from where.
Are all the options like FETK, PB-AM, etc. activated by default?

Please advise. Thanks for your help

Leo

Attached you will find the the output of the cmake command and the CMakeOutput.log

Re: [apbs-users] Questions regarding the attached message: Update Available: APBS v3.0 from Sourceforge

[Boaz S. <bsh...@bg...>]

<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#0000FF;font-family:'Times New Roman',Times,serif;" dir="ltr">
<p>Hi Nathan,</p>
<p><br>
</p>
<p>Thanks for letting me (us) know. Take your time.</p>
<p><br>
</p>
<p>Cheers,</p>
<p><br>
</p>
<p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Boaz</p>
<div id="Signature">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size: 10pt; color: rgb(0, 0, 255); font-family: &quot;Times New Roman&quot;, Times, serif, EmojiFont, &quot;Apple Color Emoji&quot;, &quot;Segoe UI Emoji&quot;, NotoColorEmoji, &quot;Segoe UI Symbol&quot;, &quot;Android Emoji&quot;, EmojiSymbols;">
<div style="font-family:Tahoma; font-size:13px">
<div><font face="Times New Roman" size="3"></font>&nbsp;</div>
<div><font face="Times New Roman" size="3"></font>&nbsp;</div>
<div><font color="#000080" face="Times New Roman" size="3"><em>Boaz Shaanan, Ph.D.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<br>
Dept. of Life Sciences&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
Ben-Gurion University of the Negev&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
Beer-Sheva 84105&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
Israel&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
E-mail: bsh...@bg...<br>
Phone: 972-8-647-2220&nbsp;&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;<br>
Fax:&nbsp;&nbsp; 972-8-647-2992 or 972-8-646-1710&nbsp;&nbsp;&nbsp;&nbsp;</em></font></div>
<div><font color="#000080" face="Times New Roman" size="3"><em></em></font>&nbsp;</div>
<div><font color="#000080" face="Times New Roman" size="3"><em></em></font>&nbsp;</div>
<div><font face="Times New Roman" size="3"><em><font color="#000080">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<br>
<br>
</font></em></font></div>
<font face="Times New Roman" size="3"></font></div>
</div>
</div>
<br>
<br>
<div style="color: rgb(0, 0, 0);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Nathan Baker &lt;nat...@gm...&gt;<br>
<b>Sent:</b> Wednesday, May 27, 2020 6:40 PM<br>
<b>To:</b> בעז שאנן<br>
<b>Cc:</b> apb...@li...<br>
<b>Subject:</b> Re: [apbs-users] Questions regarding the attached message: Update Available: APBS v3.0 from Sourceforge</font>
<div>&nbsp;</div>
</div>
<div>
<div dir="ltr">Hi Boaz --
<div><br>
</div>
<div>Sorry; I created the release and forgot to hit the &quot;delay&quot; button to give us a few days before Sourceforge sends out announcements.&nbsp; We're hoping up load the requested binaries in the next&nbsp;few days.&nbsp; I will send a message to the mailing list when those
 are posted.</div>
<div><br>
</div>
<div>Thank you,</div>
<div><br>
</div>
<div>Nathan</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May 27, 2020 at 8:33 AM Boaz Shaanan &lt;<a href="mailto:bsh...@bg...">bsh...@bg...</a>&gt; wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="ltr">
<div id="gmail-m_528719706326567988divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:rgb(0,0,255); font-family:&quot;Times New Roman&quot;,Times,serif">
<p>Hi,</p>
<p>I have questions following the attached message from Sourceforge:</p>
<p>1) Are there apbs linux and windows&nbsp;binaries available for installation?</p>
<p>2) Has the version accessible through the web gui been updated to this latest version?</p>
<p>3) Is there also an update for pdb2pqr? If so, where can I find the binary?</p>
<p><br>
</p>
<p>Thanks for your help,</p>
<p><br>
</p>
<p>Boaz</p>
<p><br>
</p>
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<div><font color="#000080" face="Times New Roman" size="3"><em>Boaz Shaanan, Ph.D.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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Ben-Gurion University of the Negev&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
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<div id="gmail-m_528719706326567988divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> SourceForge.net &lt;<a href="mailto:nor...@so..." target="_blank">nor...@so...</a>&gt;<br>
<b>Sent:</b> Tuesday, May 26, 2020 3:56 AM<br>
<b>To:</b> בעז שאנן<br>
<b>Subject:</b> Update Available: APBS</font>
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<div style="display:none">There is a new version of APBS available now. ‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;‌&nbsp;
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<b>Find</b>, <b>Create</b>, &amp; <b>Publish</b> Open Source Software for <b>free</b>.</p>
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<h1 style="font-family:Helvetica,Arial,sans-serif; font-size:18px; margin:0px; line-height:1.5em; color:rgb(255,255,255)">
Hi! You have an update available.</h1>
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<h1 style="font-family:Helvetica,Arial,sans-serif; font-size:18px; margin:0px; line-height:1.5em; color:rgb(85,85,85)">
<a href="http://l.sourceforge.net/f/a/tu8LYi2UHPfCQs8h0cgYPw~~/AAKFLwA~/RgRgrZytP0QmaHR0cHM6Ly9zb3VyY2Vmb3JnZS5uZXQvcHJvamVjdHMvYXBicy9XA3NwY0IKAEctacxeLV9Uc1ISYnNoYWFuYW5AYmd1LmFjLmlsWAQAAAAA" title="APBS" target="_blank" style="color:rgb(0,119,170); text-decoration:none">APBS</a></h1>
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Biomolecular electrostatics software</p>
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APBS-3.0.0_Programmer-Guide.zip</div>
<div id="gmail-m_528719706326567988release-date" style="font-family:Helvetica,Arial,sans-serif; font-size:11px; color:rgb(170,170,170)">
Released on 2020-05-25</div>
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Re: [apbs-users] Questions regarding the attached message: Update Available: APBS v3.0 from Sourceforge

[Nathan B. <nat...@gm...>]

Hi Boaz --

Sorry; I created the release and forgot to hit the "delay" button to give
us a few days before Sourceforge sends out announcements.  We're hoping up
load the requested binaries in the next few days.  I will send a message to
the mailing list when those are posted.

Thank you,

Nathan


On Wed, May 27, 2020 at 8:33 AM Boaz Shaanan <bsh...@bg...> wrote:

> Hi,
>
> I have questions following the attached message from Sourceforge:
>
> 1) Are there apbs linux and windows binaries available for installation?
>
> 2) Has the version accessible through the web gui been updated to this
> latest version?
>
> 3) Is there also an update for pdb2pqr? If so, where can I find the binary?
>
>
> Thanks for your help,
>
>
> Boaz
>
>
>
>
>
>
>
>
>
>
>
>
> *Boaz Shaanan, Ph.D.                                         Dept. of Life
> Sciences                                      Ben-Gurion University of the
> Negev                          Beer-Sheva
> 84105
> Israel
>                                                             E-mail:
> bsh...@bg... <bsh...@bg...> Phone: 972-8-647-2220
>        Fax:   972-8-647-2992 or 972-8-646-1710    *
>
>
>
>
>
>
>
> ------------------------------
> *From:* SourceForge.net <nor...@so...>
> *Sent:* Tuesday, May 26, 2020 3:56 AM
> *To:* בעז שאנן
> *Subject:* Update Available: APBS
>
> There is a new version of APBS available now.
> ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌
> [image: SourceForge]
> <http://l.sourceforge.net/f/a/DiQrfPJDr3Xxg_GavIeCRg~~/AAKFLwA~/RgRgrZytP0QXaHR0cHM6Ly9zb3VyY2Vmb3JnZS5uZXRXA3NwY0IKAEctacxeLV9Uc1ISYnNoYWFuYW5AYmd1LmFjLmlsWAQAAAAA>
>
> *Find*, *Create*, & *Publish* Open Source Software for *free*.
> Hi! You have an update available.
> [image: Logo]
> <http://l.sourceforge.net/f/a/tu8LYi2UHPfCQs8h0cgYPw~~/AAKFLwA~/RgRgrZytP0QmaHR0cHM6Ly9zb3VyY2Vmb3JnZS5uZXQvcHJvamVjdHMvYXBicy9XA3NwY0IKAEctacxeLV9Uc1ISYnNoYWFuYW5AYmd1LmFjLmlsWAQAAAAA>
> APBS
> <http://l.sourceforge.net/f/a/tu8LYi2UHPfCQs8h0cgYPw~~/AAKFLwA~/RgRgrZytP0QmaHR0cHM6Ly9zb3VyY2Vmb3JnZS5uZXQvcHJvamVjdHMvYXBicy9XA3NwY0IKAEctacxeLV9Uc1ISYnNoYWFuYW5AYmd1LmFjLmlsWAQAAAAA>
>
> Biomolecular electrostatics software
>
> APBS-3.0.0_Programmer-Guide.zip
> Released on 2020-05-25
>
> Download Latest Version
> <http://l.sourceforge.net/f/a/GDv5Q39x8xHkCJsgLlzphw~~/AAKFLwA~/RgRgrZytP0R4aHR0cHM6Ly9zb3VyY2Vmb3JnZS5uZXQvcHJvamVjdHMvYXBicy9maWxlcy9sYXRlc3QvZG93bmxvYWQ_dXRtX2NhbXBhaWduPXVwZGF0ZXImdXRtX21lZGl1bT1lbWFpbCZ1dG1fc291cmNlPXN1YnNjcmliZXJzVwNzcGNCCgBHLWnMXi1fVHNSEmJzaGFhbmFuQGJndS5hYy5pbFgEAAAAAA~~>
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[apbs-users] Questions regarding the attached message: Update Available: APBS v3.0 from Sourceforge

[Boaz S. <bsh...@bg...>]

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<p>Hi,</p>
<p>I have questions following the attached message from Sourceforge:</p>
<p>1) Are there apbs linux and windows&nbsp;binaries available for installation?</p>
<p>2) Has the version accessible through the web gui been updated to this latest version?</p>
<p>3) Is there also an update for pdb2pqr? If so, where can I find the binary?</p>
<p><br>
</p>
<p>Thanks for your help,</p>
<p><br>
</p>
<p>Boaz</p>
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</p>
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<div><font color="#000080" face="Times New Roman" size="3"><em>Boaz Shaanan, Ph.D.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<br>
Dept. of Life Sciences&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
Ben-Gurion University of the Negev&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
Beer-Sheva 84105&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
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E-mail: bsh...@bg...<br>
Phone: 972-8-647-2220&nbsp;&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;<br>
Fax:&nbsp;&nbsp; 972-8-647-2992 or 972-8-646-1710&nbsp;&nbsp;&nbsp;&nbsp;</em></font></div>
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<b>Sent:</b> Tuesday, May 26, 2020 3:56 AM<br>
<b>To:</b> בעז שאנן<br>
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Re: [apbs-users] pKa shift of ASP66 in Lysozyme

[Nathan B. <nat...@gm...>]

Hi Yuchun --

This is a very out of date web page; I was unaware it still existed.  A lot
has changed since the page was created so I am not surprised the answers
are different.  I would recommend using our more recent documentation (
http://www.poissonboltzmann.org/) and examples (
https://github.com/Electrostatics/apbs-pdb2pqr/tree/master/apbs/examples).

Thank you,

Nathan


On Mon, May 11, 2020 at 2:55 PM Yuchun Lin <y-...@ut...> wrote:

> Hi everyone,
>
> I just download APBS in from source forge and try calculate pKa from this
> website:
>
> https://sites.google.com/a/poissonboltzmann.org/software/apbs/examples/pka-calculations/lysozyme-pka-example
>
> Using exactly the same input downloaded in the website except for changing
> the path of apbs in Run-apbs.sh, but I get
> pKa shift FROM TOTAL ENERGY = -3.21045952566
>
> I expect the value should be around 2, based on the value on the website.
> Is this pKa value I got above the same as other people's results?
>
> Thank you very much for your help in advance!
>
> Best,
>
> Yu-Chun Lin
>
> --
> Best,
>
> *Yu-Chun Lin*, PhD Student
> The University of Texas at Austin | Department of Chemistry|
> https://cm.utexas.edu/
> _______________________________________________
> apbs-users mailing list
> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users
>

[apbs-users] pKa shift of ASP66 in Lysozyme

[Yuchun L. <y-...@ut...>]

Hi everyone,

I just download APBS in from source forge and try calculate pKa from this
website:
https://sites.google.com/a/poissonboltzmann.org/software/apbs/examples/pka-calculations/lysozyme-pka-example

Using exactly the same input downloaded in the website except for changing
the path of apbs in Run-apbs.sh, but I get
pKa shift FROM TOTAL ENERGY = -3.21045952566

I expect the value should be around 2, based on the value on the website.
Is this pKa value I got above the same as other people's results?

Thank you very much for your help in advance!

Best,

Yu-Chun Lin

-- 
Best,

*Yu-Chun Lin*, PhD Student
The University of Texas at Austin | Department of Chemistry|
https://cm.utexas.edu/

[apbs-users] Cloud-based APBS and PDB2PQR

[Nathan B. <nat...@gm...>]

Hi APBS & PDB2PQR users -

We would appreciate your help testing a new cloud-based version of APBS and PDB2PQR at http://apbs-rest-test.westus2.cloudapp.azure.com.

This version is intended to eventually replace the web-based APBS/PDB2PQR instance currently hosted by NBCR.  The process of moving APBS/PDB2PQR to a cloud-based architecture has triggered a redesign of the interface.  We would appreciate your feedback on both the functionality of the new cloud-based service as well as the new web interface.  Please provide feedback to me directly (nat...@gm...<mailto:nat...@gm...>), via the pdb...@li...<mailto:pdb...@li...> or apb...@li...<mailto:apb...@li...> mailing lists, or through the GitHub Issues page (https://github.com/Electrostatics/apbs-pdb2pqr/issues).

If you have not already signed up, please register your use of the software at http://eepurl.com/by4eQr.

Thank you very much for your feedback and continued support of the APBS/PDB2PQR software.

Sincerely,

Nathan Baker

Re: [apbs-users] Determining Electrostatic Potential Per Protein Residue

[Nathan B. <nat...@gm...>]

Hello -

Can you please send us your current APBS input file?

Thank you,

Nathan


On Wed, Dec 4, 2019 at 1:30 PM Neel Sanghvi <nsa...@te...>
wrote:

> Greetings all,
>
> I apologize if this has been asked before, but after browsing through
> previous queries in the mailing list, I could not find an appropriate
> response.
>
> I am using the PDB2PQR/ABPS online server in order to generate the
> electrostatic potential energy for a protein. I am using all of the default
> setting for ABPS EXCEPT that I request the potential energy per atom of the
> protein instead of the default total electrostatic potential.
>
> I then have the output for the potential energy per atom from the stdout
> file, however, I am hoping to get the potential energy PER protein RESIDUE
> instead of per atom. Can you tell me how to generate those values? I am
> able to download ABPS if need be, but I would not know how to get the
> energy per residue from there.
>
> I tried adding up the energy values for atoms of a specific residue and
> treating that sum as the energy for that residue, however, it seems as
> though if I add up the individual atomic potentials from the output file, I
> do not get the same result as the "total electrostatic energy" number in
> that same file. I wonder if this is because of double-counting of energies
> between atoms of the protein?
> If yes, then how do I account for this to get the correct energies?
>
> With great gratitude,
> Neel Sanghvi
> Matysiak Molecular Modeling Lab
> University of Maryland, College Park
>
>
> _______________________________________________
> apbs-users mailing list
> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users
>

[apbs-users] Determining Electrostatic Potential Per Protein Residue

[Neel S. <nsa...@te...>]

Greetings all,

I apologize if this has been asked before, but after browsing through
previous queries in the mailing list, I could not find an appropriate
response.

I am using the PDB2PQR/ABPS online server in order to generate the
electrostatic potential energy for a protein. I am using all of the default
setting for ABPS EXCEPT that I request the potential energy per atom of the
protein instead of the default total electrostatic potential.

I then have the output for the potential energy per atom from the stdout
file, however, I am hoping to get the potential energy PER protein RESIDUE
instead of per atom. Can you tell me how to generate those values? I am
able to download ABPS if need be, but I would not know how to get the
energy per residue from there.

I tried adding up the energy values for atoms of a specific residue and
treating that sum as the energy for that residue, however, it seems as
though if I add up the individual atomic potentials from the output file, I
do not get the same result as the "total electrostatic energy" number in
that same file. I wonder if this is because of double-counting of energies
between atoms of the protein?
If yes, then how do I account for this to get the correct energies?

With great gratitude,
Neel Sanghvi
Matysiak Molecular Modeling Lab
University of Maryland, College Park

Re: [apbs-users] Contradictory mobile ion effect on electrostatic surface

[Boaz S. <bsh...@bg...>]

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<div dir="auto">You can look into the log file of the apbs run which goes into the reply log of chimera. Maybe something will pop up.
<div dir="auto">Boaz<br>
<br>
<div dir="auto">Boaz Shaanan, Ph.D.<br>
Department of Life Sciences<br>
Ben Gurion University of the Negev<br>
Beer Sheva<br>
Israel</div>
</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Sep 10, 2019 00:37, &quot;Jun, Se-Young&quot; &lt;ju...@mi...&gt; wrote:<br type="attribution">
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<p>Hello Dr. Shaanan,</p>
<p><br>
</p>
<p>Thank you for the reply. Dielectric constants&nbsp;I used were 2.0 for protein (solute) and 78.54 for solvent.</p>
<p>I just tried and 'set' full range of surface values and got -75.16 to 10.22 for 0.15M salt and -1.021e&#43;7 to 7. I guess there are charge shielding happening for positive charge but the negative charge value is unrealistic.</p>
<p>&nbsp;</p>
<p><br>
</p>
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<p><font face="Calibri, Helvetica, sans-serif, serif, EmojiFont" size="2">Se-Young Jun, Ph.D</font><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">117 Schweitzer Hall</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">University of Missouri</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">Columbia, MO 65211</span><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Boaz Shaanan &lt;bsh...@bg...&gt;<br>
<b>Sent:</b> Monday, September 9, 2019 3:45:17 PM<br>
<b>To:</b> Jun, Se-Young<br>
<b>Cc:</b> apb...@li...<br>
<b>Subject:</b> Re: [apbs-users] Contradictory mobile ion effect on electrostatic surface</font>
<div>&nbsp;</div>
</div>
<div>
<div dir="auto">Hi,&nbsp;
<div dir="auto">When you display the electrostatic surface in chimera try first to use the option of 'show full range of values'. This is the best way to monitor and compare the effect of salt. Following that you can also use the option of showing the values
 as you move the mouse across the surface and monitor the values.&nbsp;</div>
<div dir="auto"><br>
</div>
<div dir="auto">What values do you use in apbs for the dielectric constants for the protein and solvent?</div>
<div dir="auto">Hope this helps.</div>
<div dir="auto">Boaz<br>
<br>
<div dir="auto">Boaz Shaanan, Ph.D.<br>
Department of Life Sciences<br>
Ben Gurion University of the Negev<br>
Beer Sheva<br>
Israel</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sep 9, 2019 21:47, &quot;Jun, Se-Young&quot; &lt;ju...@mi...&gt; wrote:<br type="attribution">
</div>
</div>
<div>
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Helvetica,sans-serif">
<p>Hello all,</p>
<p><br>
</p>
<p>I'm trying to generate electrostatic surface of a protein using UCSF Chimera but the surface charge doesn't&nbsp;seems to&nbsp;correlate with mobile ion concentrations in a right way.</p>
<p>I used PDB2PQR and APBS that are included in Chimera software package.&nbsp;<span style="font-size:12pt">For PDB2PQR, default option was used with PARSE. For APBS, mobile ions&nbsp;were included to the default setting where the mobile&nbsp;</span><span style="font-size:12pt">ions
 were sodium ion&nbsp;</span><span style="font-size:12pt">of &#43;1 charge and 0.9 radius, and chloride ion with -1 charge and 1.8 radius. Calculation was
</span>executed<span style="font-size:12pt">&nbsp;for two different mobile ion concentrations; 0.15M and 2M.&nbsp;</span></p>
<p><span style="font-size:12pt">I have </span>successfully<span style="font-size:12pt">&nbsp;applied the generate&nbsp;.dx files on the molecular surface for electrostatic coloring. However, the problem is, I was expecting the protein&nbsp;surface to be less charged at higher
 mobile ion concentration due to charge shielding. However, result that I got show more intense protein surface&nbsp;coloring with 2M salt than 0.15M.&nbsp;</span></p>
<p><span style="font-size:12pt">Am I doing something wrong?&nbsp;</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Sincerely,</span></p>
<p><br>
</p>
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<p><font face="Calibri, Helvetica, sans-serif, serif, EmojiFont" size="2">Se-Young Jun, Ph.D</font><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">117 Schweitzer Hall</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">University of Missouri</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">Columbia, MO 65211</span><br>
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Re: [apbs-users] Contradictory mobile ion effect on electrostatic surface

[Boaz S. <bsh...@bg...>]

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<div dir="auto">I see. So maybe something in the apbs run needs fixing.
<div dir="auto">Boaz<br>
<br>
<div dir="auto">Boaz Shaanan, Ph.D.<br>
Department of Life Sciences<br>
Ben Gurion University of the Negev<br>
Beer Sheva<br>
Israel</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sep 10, 2019 00:37, &quot;Jun, Se-Young&quot; &lt;ju...@mi...&gt; wrote:<br type="attribution">
</div>
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<p>Hello Dr. Shaanan,</p>
<p><br>
</p>
<p>Thank you for the reply. Dielectric constants&nbsp;I used were 2.0 for protein (solute) and 78.54 for solvent.</p>
<p>I just tried and 'set' full range of surface values and got -75.16 to 10.22 for 0.15M salt and -1.021e&#43;7 to 7. I guess there are charge shielding happening for positive charge but the negative charge value is unrealistic.</p>
<p>&nbsp;</p>
<p><br>
</p>
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<p><font face="Calibri, Helvetica, sans-serif, serif, EmojiFont" size="2">Se-Young Jun, Ph.D</font><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">117 Schweitzer Hall</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">University of Missouri</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">Columbia, MO 65211</span><br>
</p>
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<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Boaz Shaanan &lt;bsh...@bg...&gt;<br>
<b>Sent:</b> Monday, September 9, 2019 3:45:17 PM<br>
<b>To:</b> Jun, Se-Young<br>
<b>Cc:</b> apb...@li...<br>
<b>Subject:</b> Re: [apbs-users] Contradictory mobile ion effect on electrostatic surface</font>
<div>&nbsp;</div>
</div>
<div>
<div dir="auto">Hi,&nbsp;
<div dir="auto">When you display the electrostatic surface in chimera try first to use the option of 'show full range of values'. This is the best way to monitor and compare the effect of salt. Following that you can also use the option of showing the values
 as you move the mouse across the surface and monitor the values.&nbsp;</div>
<div dir="auto"><br>
</div>
<div dir="auto">What values do you use in apbs for the dielectric constants for the protein and solvent?</div>
<div dir="auto">Hope this helps.</div>
<div dir="auto">Boaz<br>
<br>
<div dir="auto">Boaz Shaanan, Ph.D.<br>
Department of Life Sciences<br>
Ben Gurion University of the Negev<br>
Beer Sheva<br>
Israel</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sep 9, 2019 21:47, &quot;Jun, Se-Young&quot; &lt;ju...@mi...&gt; wrote:<br type="attribution">
</div>
</div>
<div>
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Helvetica,sans-serif">
<p>Hello all,</p>
<p><br>
</p>
<p>I'm trying to generate electrostatic surface of a protein using UCSF Chimera but the surface charge doesn't&nbsp;seems to&nbsp;correlate with mobile ion concentrations in a right way.</p>
<p>I used PDB2PQR and APBS that are included in Chimera software package.&nbsp;<span style="font-size:12pt">For PDB2PQR, default option was used with PARSE. For APBS, mobile ions&nbsp;were included to the default setting where the mobile&nbsp;</span><span style="font-size:12pt">ions
 were sodium ion&nbsp;</span><span style="font-size:12pt">of &#43;1 charge and 0.9 radius, and chloride ion with -1 charge and 1.8 radius. Calculation was
</span>executed<span style="font-size:12pt">&nbsp;for two different mobile ion concentrations; 0.15M and 2M.&nbsp;</span></p>
<p><span style="font-size:12pt">I have </span>successfully<span style="font-size:12pt">&nbsp;applied the generate&nbsp;.dx files on the molecular surface for electrostatic coloring. However, the problem is, I was expecting the protein&nbsp;surface to be less charged at higher
 mobile ion concentration due to charge shielding. However, result that I got show more intense protein surface&nbsp;coloring with 2M salt than 0.15M.&nbsp;</span></p>
<p><span style="font-size:12pt">Am I doing something wrong?&nbsp;</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Sincerely,</span></p>
<p><br>
</p>
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<p><font face="Calibri, Helvetica, sans-serif, serif, EmojiFont" size="2">Se-Young Jun, Ph.D</font><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">117 Schweitzer Hall</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">University of Missouri</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">Columbia, MO 65211</span><br>
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Re: [apbs-users] Contradictory mobile ion effect on electrostatic surface

[Jun, Se-Y. <ju...@mi...>]

Hello Dr. Shaanan,


Thank you for the reply. Dielectric constants I used were 2.0 for protein (solute) and 78.54 for solvent.

I just tried and 'set' full range of surface values and got -75.16 to 10.22 for 0.15M salt and -1.021e+7 to 7. I guess there are charge shielding happening for positive charge but the negative charge value is unrealistic.




Se-Young Jun, Ph.D
117 Schweitzer Hall
University of Missouri
Columbia, MO 65211

________________________________
From: Boaz Shaanan <bsh...@bg...>
Sent: Monday, September 9, 2019 3:45:17 PM
To: Jun, Se-Young
Cc: apb...@li...
Subject: Re: [apbs-users] Contradictory mobile ion effect on electrostatic surface

Hi,
When you display the electrostatic surface in chimera try first to use the option of 'show full range of values'. This is the best way to monitor and compare the effect of salt. Following that you can also use the option of showing the values as you move the mouse across the surface and monitor the values.

What values do you use in apbs for the dielectric constants for the protein and solvent?
Hope this helps.
Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel

On Sep 9, 2019 21:47, "Jun, Se-Young" <ju...@mi...> wrote:

Hello all,


I'm trying to generate electrostatic surface of a protein using UCSF Chimera but the surface charge doesn't seems to correlate with mobile ion concentrations in a right way.

I used PDB2PQR and APBS that are included in Chimera software package. For PDB2PQR, default option was used with PARSE. For APBS, mobile ions were included to the default setting where the mobile ions were sodium ion of +1 charge and 0.9 radius, and chloride ion with -1 charge and 1.8 radius. Calculation was executed for two different mobile ion concentrations; 0.15M and 2M.

I have successfully applied the generate .dx files on the molecular surface for electrostatic coloring. However, the problem is, I was expecting the protein surface to be less charged at higher mobile ion concentration due to charge shielding. However, result that I got show more intense protein surface coloring with 2M salt than 0.15M.

Am I doing something wrong?


Sincerely,


Se-Young Jun, Ph.D
117 Schweitzer Hall
University of Missouri
Columbia, MO 65211

Re: [apbs-users] Contradictory mobile ion effect on electrostatic surface

[Boaz S. <bsh...@bg...>]

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<head>
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<meta content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none">
<!--
p
	{margin-top:0;
	margin-bottom:0}
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</head>
<body dir="ltr">
<div dir="auto">Hi,&nbsp;
<div dir="auto">When you display the electrostatic surface in chimera try first to use the option of 'show full range of values'. This is the best way to monitor and compare the effect of salt. Following that you can also use the option of showing the values
 as you move the mouse across the surface and monitor the values.&nbsp;</div>
<div dir="auto"><br>
</div>
<div dir="auto">What values do you use in apbs for the dielectric constants for the protein and solvent?</div>
<div dir="auto">Hope this helps.</div>
<div dir="auto">Boaz<br>
<br>
<div dir="auto">Boaz Shaanan, Ph.D.<br>
Department of Life Sciences<br>
Ben Gurion University of the Negev<br>
Beer Sheva<br>
Israel</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sep 9, 2019 21:47, &quot;Jun, Se-Young&quot; &lt;ju...@mi...&gt; wrote:<br type="attribution">
</div>
</div>
<div>
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Helvetica,sans-serif">
<p>Hello all,</p>
<p><br>
</p>
<p>I'm trying to generate electrostatic surface of a protein using UCSF Chimera but the surface charge doesn't&nbsp;seems to&nbsp;correlate with mobile ion concentrations in a right way.</p>
<p>I used PDB2PQR and APBS that are included in Chimera software package.&nbsp;<span style="font-size:12pt">For PDB2PQR, default option was used with PARSE. For APBS, mobile ions&nbsp;were included to the default setting where the mobile&nbsp;</span><span style="font-size:12pt">ions
 were sodium ion&nbsp;</span><span style="font-size:12pt">of &#43;1 charge and 0.9 radius, and chloride ion with -1 charge and 1.8 radius. Calculation was
</span>executed<span style="font-size:12pt">&nbsp;for two different mobile ion concentrations; 0.15M and 2M.&nbsp;</span></p>
<p><span style="font-size:12pt">I have </span>successfully<span style="font-size:12pt">&nbsp;applied the generate&nbsp;.dx files on the molecular surface for electrostatic coloring. However, the problem is, I was expecting the protein&nbsp;surface to be less charged at higher
 mobile ion concentration due to charge shielding. However, result that I got show more intense protein surface&nbsp;coloring with 2M salt than 0.15M.&nbsp;</span></p>
<p><span style="font-size:12pt">Am I doing something wrong?&nbsp;</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Sincerely,</span></p>
<p><br>
</p>
<div id="Signature">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif,EmojiFont,&quot;Apple Color Emoji&quot;,&quot;Segoe UI Emoji&quot;,NotoColorEmoji,&quot;Segoe UI Symbol&quot;,&quot;Android Emoji&quot;,EmojiSymbols">
<p><font face="Calibri, Helvetica, sans-serif, serif, EmojiFont" size="2">Se-Young Jun, Ph.D</font><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">117 Schweitzer Hall</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">University of Missouri</span><br style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">
<span style="font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont; font-size:small">Columbia, MO 65211</span><br>
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