VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jan 22 2008 - 20:00:40 CST

Hi Lucas,
I don't see any place where you read in a topology file, and your pdb
doesn't seem to have a residue name for your atom. Both are needed if
you want to generate a psf. You may want to have a look at the namd
tutorial
(http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html)
and the psfgen manual for more.

Also, just as a side note, psfgen and autopsf are two separate (but
related) entities; psfgen is the engine used by vmd/namd for generating
psfs, whereas autopsf is a gui for psfgen in vmd that allows access to a
subset of psfgen's features. It looks like you're just using psfgen here.

Best,
Peter

Lucas Fernández Seivane wrote:
> 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
>>