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.
On Thu, Oct 10, 2013 at 11:20 AM, Lane Votapka <email@example.com> wrote:
- If I load a dummy PQR file with an atom of zero charge & radius, then I get a field full of 'nan's- If I load a dummy PQR file with an atom that has a nonzero charge/radius, I get an electrostatic map for that single atomHi Nathan,- 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
I tried the suggestion above, however APBS seems to ignore the loaded meshes and generate its own meshes based on the PQR file.
Here is my APBS input file:
mol pqr dummy.pqr
charge dx mycharge.dx
diel dx mydielx.dx mydiely.dx mydielz.dx
kappa dx mykappa.dx
dime 193 193 225
cglen 103.4664 110.9860 152.3768
fglen 97.0302 100.4482 119.2622
cgcent mol 1
fgcent mol 1
ion charge -1.00 conc 0.150 radius 1.8150
ion charge 1.00 conc 0.150 radius 1.8750
write pot dx fastee_all
-LaneOn Thu, Oct 10, 2013 at 10:25 AM, Lane Votapka <firstname.lastname@example.org> wrote:
Thanks Nathan! I'll give that a try-LaneOn 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?
Pacific Northwest National Laboratory
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.
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