VMD-L Mailing List

From: Rene Prieto (rene.prietoch_at_gmail.com)
Date: Mon Jul 21 2008 - 18:25:52 CDT

Hi everyone.

I have a lipid that I want to solvate. In order to solvate it, I know that I
need both PSF and PDB files. But when I try to create the PSF, starting from
the PDB file, with the command:

set sel [atomselect top "all"]
$sel writespf molecule.psf

The program just doesn't create the angles nor dihedrals. It just creates
the bonds in the PSF file. And when I solvate it, it just doesn't appear my
molecule, due to missing angles and dihedrals.

I already read psfgen, but it i'm very confused. I'm having a hard time
trying to figure out the commands. I also tried to add angles and dihedrals
manually, but it seems to be a very painful way to do it.
To check if something was wrong with my PDB, i did the same process with
UBQ, the tutorial molecule, and in UBQ.PSF didn't appear the angles and
dihedrals.

My question is, what can I do to create my angles and dihedrals in my PSF
file? or how can I generate a PSF file with the correct angles and
dihedrals?

Cheers,
Rene Prieto-Chacon