VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Mon Jul 21 2008 - 19:04:44 CDT

why not trying to do it like described in the tutorial you are
referring to?
in the first section of the namd tutorial it is exactly described how
to generate psf files.
Figure 2 in this tutorial shows also the logics in generating psf files

you could also use the automatic psf builder in vmd.

apart from that, you should check if the lipid you are using is
parametrized.

eddi

On Jul 21, 2008, at 6:25 PM, Rene Prieto wrote:

> 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