Thanks Nuo, that seemed to work!

Best,
-Lane


On Fri, Oct 18, 2013 at 9:35 AM, Nuo Wang <wolich22@gmail.com> wrote:
You have to use this keyword:http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/elec-input-file-section/elec-keywords/usemap

Nuo


On Fri, Oct 18, 2013 at 9:04 AM, Lane Votapka <lvotapka100@gmail.com> wrote:
Hello All,

I was wondering if anyone got a chance to think about the message above that I sent: even using dummy atoms didn't allow me to perform calculations on the meshes with APBS.

Best,
-Lane


On Thu, Oct 10, 2013 at 11:20 AM, Lane Votapka <lvotapka100@gmail.com> wrote:
Hi Nathan,

I tried the suggestion above, however APBS seems to ignore the loaded meshes and generate its own meshes based on the PQR file.

For instance:
- If I load a dummy PQR file with no atoms, I get a VASSERT error that the number of atoms must be greater than 0
- If I load a dummy PQR file with an atom that has a nonzero charge/radius, I get an electrostatic map for that single atom
- If I load a dummy PQR file with an atom of zero charge & radius, then I get a field full of 'nan's

Here is my APBS input file:

read
mol pqr dummy.pqr
charge dx mycharge.dx
diel dx mydielx.dx mydiely.dx mydielz.dx
kappa dx mykappa.dx
end
elec
mg-auto
dime 193 193 225
cglen 103.4664 110.9860 152.3768
fglen 97.0302 100.4482 119.2622
cgcent mol 1
fgcent mol 1
lpbe
bcfl sdh
ion charge -1.00 conc 0.150 radius 1.8150
ion charge 1.00 conc 0.150 radius 1.8750
mol 1
pdie 2.0
sdie 78.54
srfm smol
chgm spl2
sdens 10.00
srad 1.40
swin 0.30
temp 300
calcforce no
write pot dx fastee_all
end
quit

-Lane


On Thu, Oct 10, 2013 at 10:25 AM, Lane Votapka <lvotapka100@gmail.com> wrote:
Thanks Nathan! I'll give that a try

-Lane


On Wed, Oct 9, 2013 at 7:12 PM, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:

Hi Lane

You should be able to load a dummy molecule to circumvent this issue.

Andrew, can you please add this to the JIRA list of future APBS features?

Thanks,

--

Nathan Baker

Laboratory Fellow

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

From: Lane Votapka [mailto:lvotapka100@gmail.com]
Sent: Tuesday, October 08, 2013 2:50 PM
To: apbs-users@lists.sourceforge.net
Subject: [apbs-users] loading my own charge, kappa, diel meshes

Hello APBS users/developers,

I'm trying to use APBS to run after loading in custom kappa, dielx/y/z, and charge meshes. I don't have a molecule to load because I only want it to use the meshes I've given it. How can I run APBS so it doesn't need a PQR or PDB file to run the electrostatics.

Best,

-Lane





------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
_______________________________________________
apbs-users mailing list
apbs-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/apbs-users