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