VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jul 21 2008 - 19:31:48 CDT

On Mon, 21 Jul 2008, Rene Prieto wrote:

RP> Hi everyone.
RP>
RP> I have a lipid that I want to solvate. In order to solvate it, I know that I
RP> need both PSF and PDB files. But when I try to create the PSF, starting from
RP> the PDB file, with the command:
RP>
RP> set sel [atomselect top "all"]
RP> $sel writespf molecule.psf
RP>
RP> The program just doesn't create the angles nor dihedrals. It just creates
RP> the bonds in the PSF file. And when I solvate it, it just doesn't appear my
RP> molecule, due to missing angles and dihedrals.

rene,

anything written by VMD directly will only be a partial .psf.
VMD prints a warning about this to its console (have a look!).
this is because VMD doesn't read/need/store all of the information
from a psf and thus the resulting .psf file can only be used for
visualization.

only if you load the psfgen plugin and use the respective
commands (see the psfgen tutorial) you can get a complete
.psf file.

cheers,
   axel.

RP>
RP> I already read psfgen, but it i'm very confused. I'm having a hard time
RP> trying to figure out the commands. I also tried to add angles and dihedrals
RP> manually, but it seems to be a very painful way to do it.
RP> To check if something was wrong with my PDB, i did the same process with
RP> UBQ, the tutorial molecule, and in UBQ.PSF didn't appear the angles and
RP> dihedrals.
RP>
RP> My question is, what can I do to create my angles and dihedrals in my PSF
RP> file? or how can I generate a PSF file with the correct angles and
RP> dihedrals?
RP>
RP>
RP> Cheers,
RP> Rene Prieto-Chacon
RP> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.