VMD-L Mailing List

From: Lucas Fernández Seivane (quevedin_at_gmail.com)
Date: Tue Jan 22 2008 - 16:07:50 CST

Thanks! I will explain what happens

I have created an ultra-simple .pdb:
ATOM 1 C 0 1.790 -0.725 1.471 0.11 0.00 C

Then run in psfgen.exe
vmd > ../psfgen.exe
segment C {
pdb catom.pdb
}
coordpdb catom.pdb C
writepsf test.psf
exit
PSFGEN from NAMD 2.6 for Win32-i686
% building segment C
reading residues from pdb file catom.pdb
extracted 0 residues from pdb file
Info: generating structure...
Info: segment complete.
% reading coordinates from pdb file catom.pdb for segment C
no residue of segment C
Warning: failed to set coordinate for atom C : C
% Info: writing psf file test.psf
total of 0 atoms
total of 0 bonds
total of 0 angles
total of 0 dihedrals
total of 0 impropers
total of 0 cross-terms
Info: psf file complete.
%
and I get a .psf with 0 atoms...
What am I doing wrong?

Thanks!
Lucas
Peter Freddolino wrote:
> You're not trying to do the impossible. However, if something is going
> wrong, telling us exactly what you did, and what error you encounter
> would greatly help in figuring out what is causing your problem.
>
> Best,
> Peter
>
> Lucas Fernández Seivane wrote:
>> Hi everybody
>>
>> I am trying to build an extremely simple model of just one atom
>> solvated, but I cannot generate the .psf with the autopsf feature. Am
>> I tring to do something impossible?
>>
>> all the best
>>
>> Lucas
>