pdb2pqr-users — A list for discussion of PDB2PQR, troubleshooting, and reporting potential bugs

Re: [Pdb2pqr-users] Fw: This mailing list is shutting down

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

Thanks Boaz!

Robert

On Thu, Dec 10, 2020 at 05:00:56PM +0000, Boaz Shaanan wrote:
>   Hi Robert,
>
>   I'm not sure but perhaps you'd have to send your message to the list
>   mentioned below, which appears to be the current one for apbs-pdb2pqr
>   users (according to the attached message).
>
>   Stay safe.
>
>   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
>
>
>     __________________________________________________________________
>
>   From: Baker, Nathan via pdb2pqr-users
>   <pdb...@li...>
>   Sent: Friday, September 25, 2020 5:07 AM
>   To: PDB2PQR Mailing List
>   Subject: [Pdb2pqr-users] This mailing list is shutting down
>
>   Hi All –
>
>
>   This mailing list is shutting down.  Please use
>   [1]https://github.com/Electrostatics/pdb2pqr/issues for user support.
>   [2][6935492?s=400&amp;v=4]
>   [3]Issues · Electrostatics/pdb2pqr · GitHub
>   github.com
>   PDB2PQR - determining titration states, adding missing atoms, and
>   assigning charges/radii to biomolecules. - Electrostatics/pdb2pqr
>
>
>   Thank you,
>
>
>   --
>   Nathan Baker
>   [4]http://pronoun.is/he
>   [5]Pronoun Island: he/him examples
>   pronoun.is
>   Here are some example sentences using my he/him pronouns: He went to
>   the park. I went with him . He brought his frisbee. At least I think it
>   was his . He threw the frisbee to himself .
>   Physical and Computational Sciences Directorate — Pacific Northwest
>   Natl Lab
>   Department of Applied Mathematics — University of Washington
>   [6]https://www.linkedin.com/in/nathanandrewbaker/
>
>References
>
>   1. https://urldefense.com/v3/__https://github.com/Electrostatics/pdb2pqr/issues__;!!Mih3wA!X681kE55JJEMETWG1GI8ly3jGQMSjMxBPZiooYh8zMezdy4tPWHZ3RporHNj$
>   2. https://urldefense.com/v3/__https://github.com/Electrostatics/pdb2pqr/issues__;!!Mih3wA!X681kE55JJEMETWG1GI8ly3jGQMSjMxBPZiooYh8zMezdy4tPWHZ3RporHNj$
>   3. https://urldefense.com/v3/__https://github.com/Electrostatics/pdb2pqr/issues__;!!Mih3wA!X681kE55JJEMETWG1GI8ly3jGQMSjMxBPZiooYh8zMezdy4tPWHZ3RporHNj$
>   4. https://urldefense.com/v3/__http://pronoun.is/he__;!!Mih3wA!X681kE55JJEMETWG1GI8ly3jGQMSjMxBPZiooYh8zMezdy4tPWHZ3cmi1XFt$
>   5. https://urldefense.com/v3/__http://pronoun.is/he__;!!Mih3wA!X681kE55JJEMETWG1GI8ly3jGQMSjMxBPZiooYh8zMezdy4tPWHZ3cmi1XFt$
>   6. https://urldefense.com/v3/__https://www.linkedin.com/in/nathanandrewbaker/__;!!Mih3wA!X681kE55JJEMETWG1GI8ly3jGQMSjMxBPZiooYh8zMezdy4tPWHZ3eBMbjHD$


>_______________________________________________
>pdb2pqr-users mailing list
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>_______________________________________________
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[Pdb2pqr-users] Server status?

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

Hi,

I'm trying to use the PDB2PQR web server 
(http://server.poissonboltzmann.org/pdb2pqr) but after clicking "Start Job" 
I get "Submitting job" message and it is just stuck there. Is this because 
of long waiting times for jobs to run? This is with both firefox and 
chrome browsers.

Thanks,

Robert

[Pdb2pqr-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/pdb2pqr/issues for user 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/

Re: [Pdb2pqr-users] AttributeError: Residue instance has no attribute 'isCterm'

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

Hello --

I apologize but I am unable to determine what is wrong with this PDB.

Do you have the same problem with server.poissonboltzmann.org?  Have you
tried running some of the PDB2PQR clean-up commands from the command line
and then trying this molecule again?

Thank you,

Nathan


On Thu, May 28, 2020 at 12:50 PM Christina Frances Sandall <
cfs...@uc...> wrote:

> Hi there,
>
> I am trying to run pdb2pqr with the pdb file I have attached, but I
> receive the following errors:
>
> ~/bin/pdb2pqr-osx-bin64-2.1.0$ ./pdb2pqr --ph-calc-method=pdb2pka
> --with-ph=7.4 --ff=parse com2119.pdb com2119.pqr
>
> --------------------------
> PDB2PQR - a Python-based structural conversion utility
> --------------------------
> Please cite your use of PDB2PQR as:
>   Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
>   PDB2PQR: an automated pipeline for the setup, execution,
>   and analysis of Poisson-Boltzmann electrostatics calculations.
>   Nucleic Acids Research 32 W665-W667 (2004).
>
> Error parsing line: '0'
> <0>
> Truncating remaining errors for record type:0
> Setting protein dielectric constant to  8
> Doing full pKa calculation
> Traceback (most recent call last):
>   File "<string>", line 62, in <module>
>   File "/Users/d3y382/tmp/main.py", line 740, in mainCommand
>   File "/Users/d3y382/tmp/main.py", line 341, in runPDB2PQR
>   File "/Users/d3y382/tmp/src/routines.py", line 1521, in runPDB2PKA
>   File "/Users/d3y382/tmp/pdb2pka/pka_routines.py", line 226, in runpKa
>   File "/Users/d3y382/tmp/pdb2pka/pka_routines.py", line 2196, in
> findTitratableGroups
> AttributeError: Residue instance has no attribute 'isCterm'
> pdb2pqr returned -1
>
> Could you offer any advice on how to fix this?  I have run pdb2pqr
> successfully on other files; it is this pdb file specifically which causes
> issues.
>
> Thanks very much,
> Christie
>
> _______________________________________________
> pdb2pqr-users mailing list
> pdb...@li...
> https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users
>

[Pdb2pqr-users] Ligand Parameterization Errors

[Christina F. S. <cfs...@uc...>]

Hi there,

I have run pdb2pqr successfully when I do not include the mol2 ligand file for parameterization, but trying to include the ligand causes the program to error.

i.e. this command runs correctly:
$ ./pdb2pqr --ph-calc-method=pdb2pka --with-ph=7.4 --ff=parse n3d.pdb n3d.pqr

but the following command returns an error:
$ ./pdb2pqr --ph-calc-method=pdb2pka --with-ph=7.4 --ff=parse --ligand=ADP_DRGFIN.mol2 n3d.pdb n3d_adp.pqr

--------------------------
PDB2PQR - a Python-based structural conversion utility
--------------------------
Please cite your use of PDB2PQR as:
  Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
  PDB2PQR: an automated pipeline for the setup, execution,
  and analysis of Poisson-Boltzmann electrostatics calculations.
  Nucleic Acids Research 32 W665-W667 (2004).

DEBUG INFO: PDBInputError /Users/d3y382/tmp/src/pdb.py: 585
Error encountered: Unable to find '@<TRIPOS>ATOM' in MOL2 file!

This mol2 file was downloaded from the PRODRG2 server (http://prodrg1.dyndns.org/) as suggested in the documentation for ligand file preparation.  I have attached the n3d.pdb and the ADP_DRGFIN.mol2 files.  If there is anything that can be done to this mol2 file to fix the error I would appreciate the insight!

Thanks very much,
Christie

[Pdb2pqr-users] AttributeError: Residue instance has no attribute 'isCterm'

[Christina F. S. <cfs...@uc...>]

Hi there,

I am trying to run pdb2pqr with the pdb file I have attached, but I receive the following errors:

~/bin/pdb2pqr-osx-bin64-2.1.0$ ./pdb2pqr --ph-calc-method=pdb2pka --with-ph=7.4 --ff=parse com2119.pdb com2119.pqr

--------------------------
PDB2PQR - a Python-based structural conversion utility
--------------------------
Please cite your use of PDB2PQR as:
  Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
  PDB2PQR: an automated pipeline for the setup, execution,
  and analysis of Poisson-Boltzmann electrostatics calculations.
  Nucleic Acids Research 32 W665-W667 (2004).

Error parsing line: '0'
<0>
Truncating remaining errors for record type:0
Setting protein dielectric constant to  8
Doing full pKa calculation
Traceback (most recent call last):
  File "<string>", line 62, in <module>
  File "/Users/d3y382/tmp/main.py", line 740, in mainCommand
  File "/Users/d3y382/tmp/main.py", line 341, in runPDB2PQR
  File "/Users/d3y382/tmp/src/routines.py", line 1521, in runPDB2PKA
  File "/Users/d3y382/tmp/pdb2pka/pka_routines.py", line 226, in runpKa
  File "/Users/d3y382/tmp/pdb2pka/pka_routines.py", line 2196, in findTitratableGroups
AttributeError: Residue instance has no attribute 'isCterm'
pdb2pqr returned -1

Could you offer any advice on how to fix this?  I have run pdb2pqr successfully on other files; it is this pdb file specifically which causes issues.

Thanks very much,
Christie

Re: [Pdb2pqr-users] Problem, page not working

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

Hi All --

Boaz is correct:  the new site for PDB2PQR is
http://server.poissonboltzmann.org/ (or http://apbs.poissonboltzmann.org or
http://pdb2pqr.poissonboltzmann.org).  You can also get the latest
information about APBS/PDB2PQR at our website:
http://www.poissonboltzmann.org.

Thank you,

Nathan

On Wed, Apr 29, 2020 at 6:52 AM Boaz Shaanan <bsh...@bg...> wrote:

> Hi,
> Apparently the pdb2pqr and apbs have been moved to another site. You may
> want to check the  messages from around 2 April on the list which addressed
> this issue.
> Stay safe,
> Boaz
>
> Boaz Shaanan, Ph.D.
> Department of Life Sciences
> Ben Gurion University of the Negev
> Beer Sheva
> Israel
>
> On Apr 29, 2020 15:35, "Hantz, Eric R." <ha...@bu...>
> wrote:
>
> Hello,
>
>
>
> I am trying to use the PDB2PQR server and have been receiving the
> following error after a few minutes: “This page isn’t working
> nbcr-22.ucsd.edu didn’t send any data. ERR_EMPTY_RESPONSE”. I have
> uploaded pdb files to the server before today without any issues.
>
>
>
> Thank you,
>
>
>
> [image: signature_813060003]
>
>
>
> Eric Hantz
>
> Graduate Teaching Assistant
>
> Biophysics Graduate Program
>
> Lindert Lab
>
> 2120 Newman Wolfrom
>
>
>
>
>
> On Apr 29, 2020 15:35, "Hantz, Eric R." <ha...@bu...>
> wrote:
>
> Hello,
>
>
>
> I am trying to use the PDB2PQR server and have been receiving the
> following error after a few minutes: “This page isn’t working
> nbcr-22.ucsd.edu didn’t send any data. ERR_EMPTY_RESPONSE”. I have
> uploaded pdb files to the server before today without any issues.
>
>
>
> Thank you,
>
>
>
> [image: signature_813060003]
>
>
>
> Eric Hantz
>
> Graduate Teaching Assistant
>
> Biophysics Graduate Program
>
> Lindert Lab
>
> 2120 Newman Wolfrom
>
>
> _______________________________________________
> pdb2pqr-users mailing list
> pdb...@li...
> https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users
>

Re: [Pdb2pqr-users] Problem, page not working

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

<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=windows-1255">
<meta content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
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</style>
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div dir="auto">
<div dir="auto">Hi,
<div dir="auto">Apparently the pdb2pqr and apbs have been moved to another site. You may want to check the&nbsp; messages from around 2 April on the list which addressed this issue.<br>
Stay safe,</div>
<div dir="auto">Boaz</div>
<div dir="auto"><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><br>
<div class="elided-text">On Apr 29, 2020 15:35, &quot;Hantz, Eric R.&quot; &lt;ha...@bu...&gt; wrote:<br type="attribution">
<blockquote style="margin:0 0 0 0.8ex; border-left:1px #ccc solid; padding-left:1ex">
<div>
<div>
<p><span style="font-size:11pt">Hello,</span></p>
<p><span style="font-size:11pt">&nbsp;</span></p>
<p><span style="font-size:11pt">I am trying to use the PDB2PQR server and have been receiving the following error after a few minutes: “This page isn’t working nbcr-22.ucsd.edu didn’t send any data. ERR_EMPTY_RESPONSE”. I have uploaded pdb files to the server
 before today without any issues. &nbsp;</span></p>
<p><span style="font-size:11pt">&nbsp;</span></p>
<p><span style="font-size:11pt">Thank you,</span></p>
<p><span style="font-size:11pt">&nbsp;</span></p>
<p><span style="font-size:10.5pt"><img src="cid:image001.png@01D61D8A.8865BEB0" alt="signature_813060003" height="52" width="251" style="width:2.6145in; height:0.5416in"></span></p>
<p><span style="font-size:10.5pt">&nbsp;</span></p>
<p><span style="font-size:10.5pt">Eric Hantz</span></p>
<p><span style="font-size:10.5pt; color:black">Graduate Teaching Assistant</span></p>
<p><span style="font-size:10.5pt; color:black">Biophysics Graduate Program</span></p>
<p><span style="font-size:10.5pt; color:black">Lindert Lab</span></p>
<p><span style="font-size:10.5pt; color:black">2120 Newman Wolfrom</span><span style="font-size:10.5pt"></span></p>
<p>&nbsp;</p>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Apr 29, 2020 15:35, &quot;Hantz, Eric R.&quot; &lt;ha...@bu...&gt; wrote:<br type="attribution">
</div>
</div>
<div>
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt">Hello,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">&nbsp;</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I am trying to use the PDB2PQR server and have been receiving the following error after a few minutes: “This page isn’t working nbcr-22.ucsd.edu didn’t send any data. ERR_EMPTY_RESPONSE”. I have uploaded pdb
 files to the server before today without any issues. &nbsp;</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">&nbsp;</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">&nbsp;</span></p>
<p class="MsoNormal"><span style="font-size:10.5pt"><img width="251" height="52" id="Picture_x0020_1" src="cid:image001.png@01D61D8A.8865BEB0" alt="signature_813060003" style="width:2.6145in; height:.5416in"></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt">&nbsp;</span></p>
<p class="MsoNormal"><span style="font-size:10.5pt">Eric Hantz</span></p>
<p class="MsoNormal"><span style="font-size:10.5pt; color:black">Graduate Teaching Assistant</span></p>
<p class="MsoNormal"><span style="font-size:10.5pt; color:black">Biophysics Graduate Program</span></p>
<p class="MsoNormal"><span style="font-size:10.5pt; color:black">Lindert Lab</span></p>
<p class="MsoNormal"><span style="font-size:10.5pt; color:black">2120 Newman Wolfrom</span><span style="font-size:10.5pt"></span></p>
<p class="MsoNormal">&nbsp;</p>
</div>
</div>
</body>
</html>

[Pdb2pqr-users] Problem, page not working

[Hantz, E. R. <ha...@bu...>]

Hello,

I am trying to use the PDB2PQR server and have been receiving the following error after a few minutes: “This page isn’t working nbcr-22.ucsd.edu didn’t send any data. ERR_EMPTY_RESPONSE”. I have uploaded pdb files to the server before today without any issues.

Thank you,

[signature_813060003]

Eric Hantz
Graduate Teaching Assistant
Biophysics Graduate Program
Lindert Lab
2120 Newman Wolfrom

[Pdb2pqr-users] Issue with Linux PDB2PQR

[Sophie S. <sop...@be...>]

Hi,

I recently installed PDB2PQR on a linux server to run a pipeline that I had
previously been running using the OSX version without issue.

However when I run the command (on the linux version):


pdb2pqr --ligand=${LIGF}.mol2 --chain ${PDB}.pqr ${COMP}.pqr --ff=amber
--with-ph=8


I get an error:

Traceback (most recent call last):

  File "<string>", line 62, in <module>

  File "main.py", line 740, in mainCommand

  File "main.py", line 275, in runPDB2PQR

  File
"/usr/local/lib/python2.7/dist-packages/PyInstaller/loader/pyimod03_importers.py",
line 389, in load_module

  File "pdb2pka/ligandclean/ligff.py", line 5, in <module>

  File
"/usr/local/lib/python2.7/dist-packages/PyInstaller/loader/pyimod03_importers.py",
line 389, in load_module

  File "pdb2pka/NEWligand_topology.py", line 16, in <module>

ImportError: Cannot import Algorithms, this may be the result of disabling
pdb2pka at configure stage!

pdb2pqr returned -1


But I was not getting this error when running the same command on the osx
version.


To install the software I simply unpacked the gunzipped tarball and then
added the directory to my path in my .bash_profile.


I seem to be able to run a simple pdb2pqr i.e.


pdb2pqr --ff=amber --chain -v --apbs-input ${PDB}.pdb ${PDB}.pqr


without issue.


I tried re-unpacking the tarball just in case I accidentally messed up the
files but this yielded the same error.


Any ideas what I'm doing wrong?


Best,

Sophie

Re: [Pdb2pqr-users] Problem to download pqr-file

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

Hello -

We responded to this question via GitHub issues:
https://github.com/Electrostatics/apbs-pdb2pqr/issues/539

Thanks,

Nathan


On Sun, Apr 19, 2020 at 6:58 AM Sara Svanberg <sar...@st...>
wrote:

> Hi!
> After running pdb2pqr generating the output files I can't download the
> pqr-file, I can only open it as a text file. How can I download it as a
> pqr-file? Thanks!
>
> Best,
> Sara
>
> _______________________________________________
> pdb2pqr-users mailing list
> pdb...@li...
> https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users
>

[Pdb2pqr-users] Problem to download pqr-file

[Sara S. <sar...@st...>]

Hi!
After running pdb2pqr generating the output files I can't download the pqr-file, I can only open it as a text file. How can I download it as a pqr-file? Thanks!

Best,
Sara

Re: [Pdb2pqr-users] Why is propka calculation giving me wrong net charge of the protein?

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

Hi Srdjan --

I don't know much about PSFgen but I thought it required specifying
particular patches to assign the protonation state to residues.

PROPKA is an empirical method that uses statistical rules to assign pKa
values of residues based on their local environment.  These pKa values are
then used to assign protonation state, ignoring potential coupling between
protonation states of nearby residues.  The method is fast and fairly
accurate but there does not yet exist a computational approach that is
accurate enough to replace experiments.

Thank you,

Nathan


On Fri, Apr 3, 2020 at 5:18 AM srdjan pusara <srd...@ho...>
wrote:

>   Hello,
>
>  I dont know if this email list is the right place for this question, but
> Ill give it a try. I have protonated BSA protein with Propka at pH=7 and
> with VMD/PSFgen and CHARMM force field (which is pH 7 by defult).
>   I got that protein had charge -13 with propka and -17 with PSFgen, while
> experimental data say that protein has charge -18.
>
>    So why did I get so much different data with Propka and PSFgen and why
> Propka values are not in agreement with experiment?
>    I can assume that calculations on new server are correct, so its the
> Propka itself and not a server?
>
>     Greetings.
> _______________________________________________
> pdb2pqr-users mailing list
> pdb...@li...
> https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users
>

Re: [Pdb2pqr-users] There was an error with your job submission, size in new server

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

Hi Marta --

Could you please provide an example that we can test to analyze the
behavior you're seeing?

Thank you,

Nathan


On Fri, Apr 3, 2020 at 5:18 AM Marta Perez Illana <mar...@cn...>
wrote:

> Hi all
>
> I was also encountering server problems this morning, and found the test
> link you mention in the mail archive, which works quite nice :)
>
> However I am having problems with big molecules that contain 3 chains and
> are around 900 residues each so 2700 aa in total... As far as I remember in
> the previous regular server there was no such a limit of molecule size??
>
> What  I am doing now is uploading the chains one by one, but it takes 3x
> more work :)
>
> Regards and thanks in advance
>
> Marta
> On 02.04.20 16:02, Baker, Nathan via pdb2pqr-users wrote:
>
> Hi Srdjan –
>
>
>
> Great!  I’m glad to hear the new web server is working.  We didn’t expect
> to switch platforms so soon but the COVID19 crisis has changed many things.
>
>
>
> Thank you for the feedback.
>
>
>
> Best wishes,
>
>
>
> --
> Nathan Baker
> Physical and Computational Sciences Directorate — Pacific Northwest Natl
> Lab
> Department of Applied Mathematics — University of Washington
> +1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/
> <https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>
>
>
>
> *From:* srdjan pusara <srd...@ho...>
> <srd...@ho...>
> *Sent:* Thursday, April 2, 2020 06:43
> *To:* Baker, Nathan <nat...@pn...> <nat...@pn...>;
> pdb...@li...
> *Subject:* Re: There was an error with your job submission
>
>
>
>   Hello,
>
>
>
>   In the meantime I have switched to
> http://apbs-rest-test.westus2.cloudapp.azure.com/
> <https://protect2.fireeye.com/v1/url?k=151c75ea-49a94b25-151c5fff-0cc47adc5e60-72c671dc389a292a&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F>
> and now everything works fine like before 🙂.
>
>
>
>    I didnt know that you have changed the website/server because 2-3 weeks
> ago I could run on previous websie without problems.
>
>
>
>    Greetings.
>
>
>
> APBS | Home
> <https://protect2.fireeye.com/v1/url?k=d8d117db-84642914-d8d13dce-0cc47adc5e60-b2928cb6be517f14&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F>
>
> Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated
> pipeline for the setup, execution, and analysis of Poisson-Boltzmann
> electrostatics calculations.
>
> apbs-rest-test.westus2.cloudapp.azure.com
>
>
>
>
> ------------------------------
>
> *From:* Baker, Nathan <nat...@pn...>
> *Sent:* Thursday, April 2, 2020 3:11 PM
> *To:* srdjan pusara <srd...@ho...>;
> pdb...@li... <pdb...@li...>
> *Subject:* RE: There was an error with your job submission
>
>
>
> Hello –
>
>
>
> I’m sorry about the problems you are experiencing.  Can you please let us
> know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/
> <https://protect2.fireeye.com/v1/url?k=57c080ce-0b75be01-57c0aadb-0cc47adc5e60-26176c0634ae0d5c&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F>
> or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this
> problem?
>
>
>
> Thank you,
>
> --
> Nathan Baker
> Physical and Computational Sciences Directorate — Pacific Northwest Natl
> Lab
> Department of Applied Mathematics — University of Washington
> +1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/
> <https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>
>
>
>
> *From:* srdjan pusara <srd...@ho...>
> *Sent:* Wednesday, April 1, 2020 07:57
> *To:* pdb...@li...
> *Subject:* [Pdb2pqr-users] There was an error with your job submission
>
>
>
>    Hello,
>
>
>
>   I am trying to run calculation on server but after I press Submit I am
> getting error: There was an error with your job submission. And this is
> repeating for whole day.
>
>
>
>    Can someone help me to resolve it? Maybe there is some problem with the
> server at the moment?
>
>
>
>     Cheers.
>
>
> _______________________________________________
> pdb2pqr-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users
>
> _______________________________________________
> pdb2pqr-users mailing list
> pdb...@li...
> https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users
>

[Pdb2pqr-users] Why is propka calculation giving me wrong net charge of the protein?

[srdjan p. <srd...@ho...>]

  Hello,

 I dont know if this email list is the right place for this question, but Ill give it a try. I have protonated BSA protein with Propka at pH=7 and with VMD/PSFgen and CHARMM force field (which is pH 7 by defult).
  I got that protein had charge -13 with propka and -17 with PSFgen, while experimental data say that protein has charge -18.

   So why did I get so much different data with Propka and PSFgen and why Propka values are not in agreement with experiment?
   I can assume that calculations on new server are correct, so its the Propka itself and not a server?

    Greetings.

Re: [Pdb2pqr-users] There was an error with your job submission

[A. R. <ri...@ho...>]

I did not know about the new site either 😊 Now everything works as it should, awesome!

Thank you so much for this service, by the way. I used to run the app locally in my machine but the server saves time and is super convenient 😊.

Cheers,


From: srdjan pusara <srd...@ho...>
Sent: 02 April 2020 14:43
To: Baker, Nathan <nat...@pn...>; pdb...@li...
Subject: Re: [Pdb2pqr-users] There was an error with your job submission

  Hello,

  In the meantime I have switched to http://apbs-rest-test.westus2.cloudapp.azure.com/ and now everything works fine like before 🙂.

   I didnt know that you have changed the website/server because 2-3 weeks ago I could run on previous websie without problems.

   Greetings.

APBS | Home<http://apbs-rest-test.westus2.cloudapp.azure.com/>
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.
apbs-rest-test.westus2.cloudapp.azure.com


________________________________
From: Baker, Nathan <nat...@pn...<mailto:nat...@pn...>>
Sent: Thursday, April 2, 2020 3:11 PM
To: srdjan pusara <srd...@ho...<mailto:srd...@ho...>>; pdb...@li...<mailto:pdb...@li...> <pdb...@li...<mailto:pdb...@li...>>
Subject: RE: There was an error with your job submission


Hello –



I’m sorry about the problems you are experiencing.  Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem?



Thank you,

--
Nathan Baker
Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
+1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/<https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>



From: srdjan pusara <srd...@ho...<mailto:srd...@ho...>>
Sent: Wednesday, April 1, 2020 07:57
To: pdb...@li...<mailto:pdb...@li...>
Subject: [Pdb2pqr-users] There was an error with your job submission



   Hello,



  I am trying to run calculation on server but after I press Submit I am getting error: There was an error with your job submission. And this is repeating for whole day.



   Can someone help me to resolve it? Maybe there is some problem with the server at the moment?



    Cheers.

Re: [Pdb2pqr-users] There was an error with your job submission, size in new server

[Marta P. I. <mar...@cn...>]

Hi all

I was also encountering server problems this morning, and found the test 
link you mention in the mail archive, which works quite nice :)

However I am having problems with big molecules that contain 3 chains 
and are around 900 residues each so 2700 aa in total... As far as I 
remember in the previous regular server there was no such a limit of 
molecule size??

What  I am doing now is uploading the chains one by one, but it takes 3x 
more work :)

Regards and thanks in advance

Marta

On 02.04.20 16:02, Baker, Nathan via pdb2pqr-users wrote:
>
> Hi Srdjan –
>
> Great!  I’m glad to hear the new web server is working.  We didn’t 
> expect to switch platforms so soon but the COVID19 crisis has changed 
> many things.
>
> Thank you for the feedback.
>
> Best wishes,
>
> --
> Nathan Baker
> Physical and Computational Sciences Directorate — Pacific Northwest 
> Natl Lab
> Department of Applied Mathematics — University of Washington
> +1-509-375-3997 —https://www.linkedin.com/in/nathanandrewbaker/ 
> <https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>
>
> *From:* srdjan pusara <srd...@ho...>
> *Sent:* Thursday, April 2, 2020 06:43
> *To:* Baker, Nathan <nat...@pn...>; 
> pdb...@li...
> *Subject:* Re: There was an error with your job submission
>
>   Hello,
>
>   In the meantime I have switched to 
> http://apbs-rest-test.westus2.cloudapp.azure.com/ 
> <https://protect2.fireeye.com/v1/url?k=151c75ea-49a94b25-151c5fff-0cc47adc5e60-72c671dc389a292a&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F> 
> and now everything works fine like before 🙂.
>
>    I didnt know that you have changed the website/server because 2-3 
> weeks ago I could run on previous websie without problems.
>
>    Greetings.
>
> APBS | Home 
> <https://protect2.fireeye.com/v1/url?k=d8d117db-84642914-d8d13dce-0cc47adc5e60-b2928cb6be517f14&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F>
>
> Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated 
> pipeline for the setup, execution, and analysis of Poisson-Boltzmann 
> electrostatics calculations.
>
> apbs-rest-test.westus2.cloudapp.azure.com
>
> ------------------------------------------------------------------------
>
> *From:*Baker, Nathan <nat...@pn... 
> <mailto:nat...@pn...>>
> *Sent:* Thursday, April 2, 2020 3:11 PM
> *To:* srdjan pusara <srd...@ho... 
> <mailto:srd...@ho...>>; 
> pdb...@li... 
> <mailto:pdb...@li...> 
> <pdb...@li... 
> <mailto:pdb...@li...>>
> *Subject:* RE: There was an error with your job submission
>
> Hello –
>
> I’m sorry about the problems you are experiencing.  Can you please let 
> us know if you are using 
> http://apbs-rest-test.westus2.cloudapp.azure.com/ 
> <https://protect2.fireeye.com/v1/url?k=57c080ce-0b75be01-57c0aadb-0cc47adc5e60-26176c0634ae0d5c&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F> 
> or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ 
> <http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/> when you encounter this problem?
>
> Thank you,
>
> --
> Nathan Baker
> Physical and Computational Sciences Directorate — Pacific Northwest 
> Natl Lab
> Department of Applied Mathematics — University of Washington
> +1-509-375-3997 —https://www.linkedin.com/in/nathanandrewbaker/ 
> <https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>
>
> *From:* srdjan pusara <srd...@ho... 
> <mailto:srd...@ho...>>
> *Sent:* Wednesday, April 1, 2020 07:57
> *To:* pdb...@li... 
> <mailto:pdb...@li...>
> *Subject:* [Pdb2pqr-users] There was an error with your job submission
>
>    Hello,
>
>   I am trying to run calculation on server but after I press Submit I 
> am getting error: There was an error with your job submission. And 
> this is repeating for whole day.
>
>    Can someone help me to resolve it? Maybe there is some problem with 
> the server at the moment?
>
>     Cheers.
>
>
>
> _______________________________________________
> pdb2pqr-users mailing list
> pdb...@li...
> https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users

Re: [Pdb2pqr-users] There was an error with your job submission

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

Hello -

I'm sorry about the problems you are experiencing.  Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem?

Thank you,
--
Nathan Baker
Physical and Computational Sciences Directorate - Pacific Northwest Natl Lab
Department of Applied Mathematics - University of Washington
+1-509-375-3997 -  https://www.linkedin.com/in/nathanandrewbaker/<https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>

From: srdjan pusara <srd...@ho...>
Sent: Wednesday, April 1, 2020 07:57
To: pdb...@li...
Subject: [Pdb2pqr-users] There was an error with your job submission

   Hello,

  I am trying to run calculation on server but after I press Submit I am getting error: There was an error with your job submission. And this is repeating for whole day.

   Can someone help me to resolve it? Maybe there is some problem with the server at the moment?

    Cheers.

Re: [Pdb2pqr-users] error submission

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

Hello –

I’m sorry about the problems you are experiencing.  Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem?

Thank you,


--
Nathan Baker
Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
+1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/<https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>

From: Melissa Hoang <mel...@gm...>
Sent: Wednesday, April 1, 2020 16:32
To: pdb...@li...
Subject: [Pdb2pqr-users] error submission

Hello,

I have been trying to upload a PDB file to the web serve, but the job error message pops up.I have tried with PDB ID as well. The submission was with its default setting.


Please Help,
An undergraduate who just wants to make it to graduation

Re: [Pdb2pqr-users] Job Submission Error

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

Hello –

I’m sorry about the problems you are experiencing.  Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem?

Thank you,

--
Nathan Baker
Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
+1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/<https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>

From: Sophie Shoemaker <sop...@be...>
Sent: Wednesday, April 1, 2020 13:25
To: pdb...@li...
Subject: [Pdb2pqr-users] Job Submission Error

Hello,

When I tried to submit a job to the PDB2PQR webserver, I get an error: "There was an error with your job submission".

This happened when I tried to do the example from the tutorial with 1FAS as well as uploading my own structure.

Is this a known issue?

Best,
Sophie

Re: [Pdb2pqr-users] Server not working?

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

Hello –

I’m sorry about the problems you are experiencing.  Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem?

Thank you,
--
Nathan Baker
Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
+1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/<https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>

From: A. Riera <ri...@ho...>
Sent: Wednesday, April 1, 2020 06:30
To: pdb...@li...
Subject: [Pdb2pqr-users] Server not working?

Hello!

I hope you are all fine 🙂. I am writing because I have encountered the following error in the PDB2PQR sever: when I submit a structure, the server always responds "There was an error with your job submission" and that is basically it. Not other details are given. I know that the PDB files are right because they worked in before. As far as I know, it has been like this for a couple of days.

Any help would be really appreciated!

Thank you so much,

Alberto

Re: [Pdb2pqr-users] There was an error with your job submission

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

Hi Srdjan –

Great!  I’m glad to hear the new web server is working.  We didn’t expect to switch platforms so soon but the COVID19 crisis has changed many things.

Thank you for the feedback.

Best wishes,

--
Nathan Baker
Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
+1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/<https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>

From: srdjan pusara <srd...@ho...>
Sent: Thursday, April 2, 2020 06:43
To: Baker, Nathan <nat...@pn...>; pdb...@li...
Subject: Re: There was an error with your job submission

  Hello,

  In the meantime I have switched to http://apbs-rest-test.westus2.cloudapp.azure.com/<https://protect2.fireeye.com/v1/url?k=151c75ea-49a94b25-151c5fff-0cc47adc5e60-72c671dc389a292a&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F> and now everything works fine like before 🙂.

   I didnt know that you have changed the website/server because 2-3 weeks ago I could run on previous websie without problems.

   Greetings.

APBS | Home<https://protect2.fireeye.com/v1/url?k=d8d117db-84642914-d8d13dce-0cc47adc5e60-b2928cb6be517f14&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F>
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.
apbs-rest-test.westus2.cloudapp.azure.com


________________________________
From: Baker, Nathan <nat...@pn...<mailto:nat...@pn...>>
Sent: Thursday, April 2, 2020 3:11 PM
To: srdjan pusara <srd...@ho...<mailto:srd...@ho...>>; pdb...@li...<mailto:pdb...@li...> <pdb...@li...<mailto:pdb...@li...>>
Subject: RE: There was an error with your job submission


Hello –



I’m sorry about the problems you are experiencing.  Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/<https://protect2.fireeye.com/v1/url?k=57c080ce-0b75be01-57c0aadb-0cc47adc5e60-26176c0634ae0d5c&q=1&e=96c8347e-2682-4eca-a93a-9a08bff0ba00&u=http%3A%2F%2Fapbs-rest-test.westus2.cloudapp.azure.com%2F> or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem?



Thank you,

--
Nathan Baker
Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
+1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/<https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>



From: srdjan pusara <srd...@ho...<mailto:srd...@ho...>>
Sent: Wednesday, April 1, 2020 07:57
To: pdb...@li...<mailto:pdb...@li...>
Subject: [Pdb2pqr-users] There was an error with your job submission



   Hello,



  I am trying to run calculation on server but after I press Submit I am getting error: There was an error with your job submission. And this is repeating for whole day.



   Can someone help me to resolve it? Maybe there is some problem with the server at the moment?



    Cheers.

Re: [Pdb2pqr-users] There was an error with your job submission

[srdjan p. <srd...@ho...>]

  Hello,

  In the meantime I have switched to http://apbs-rest-test.westus2.cloudapp.azure.com/ and now everything works fine like before 🙂.

   I didnt know that you have changed the website/server because 2-3 weeks ago I could run on previous websie without problems.

   Greetings.

APBS | Home<http://apbs-rest-test.westus2.cloudapp.azure.com/>
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.
apbs-rest-test.westus2.cloudapp.azure.com


________________________________
From: Baker, Nathan <nat...@pn...>
Sent: Thursday, April 2, 2020 3:11 PM
To: srdjan pusara <srd...@ho...>; pdb...@li... <pdb...@li...>
Subject: RE: There was an error with your job submission


Hello –



I’m sorry about the problems you are experiencing.  Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem?



Thank you,

--
Nathan Baker
Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
+1-509-375-3997 —  https://www.linkedin.com/in/nathanandrewbaker/<https://protect2.fireeye.com/v1/url?k=9c67d4e2-c0d2ea2d-9c67fef7-0cc47adc5e60-b631ee18bc35d86c&q=1&e=0ddba0e7-94b2-43d4-b16e-ad00f89cd897&u=https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnathanandrewbaker%2F>



From: srdjan pusara <srd...@ho...>
Sent: Wednesday, April 1, 2020 07:57
To: pdb...@li...
Subject: [Pdb2pqr-users] There was an error with your job submission



   Hello,



  I am trying to run calculation on server but after I press Submit I am getting error: There was an error with your job submission. And this is repeating for whole day.



   Can someone help me to resolve it? Maybe there is some problem with the server at the moment?



    Cheers.

[Pdb2pqr-users] error submission

[Melissa H. <mel...@gm...>]

Hello,

I have been trying to upload a PDB file to the web serve, but the job error
message pops up.I have tried with PDB ID as well. The submission was with
its default setting.


Please Help,
An undergraduate who just wants to make it to graduation

[Pdb2pqr-users] Job Submission Error

[Sophie S. <sop...@be...>]

Hello,

When I tried to submit a job to the PDB2PQR webserver, I get an error:
"There was an error with your job submission".

This happened when I tried to do the example from the tutorial with 1FAS as
well as uploading my own structure.

Is this a known issue?

Best,
Sophie