VMD-L Mailing List

From: Hannes Loeffler (Hannes.Loeffler_at_stfc.ac.uk)
Date: Mon Oct 11 2010 - 07:25:58 CDT

On Wed, 22 Sep 2010 13:18:45 +0200
"Jorgen Simonsen" <jorgen589_at_gmail.com> wrote:

> Hi all
>
> I am trying to generate a psf in the charmm format - no the xplor
> format. So I can generate the file using the parameter
>
> psf charmm x.psf
>
> the problem is that when I use this file further on it does not
> recognize it as a charmm psf file - I do not have access to charmm
> but should they not be identical?

PSF files generated by psfgen are not fully compatible with CHARMM
generated files. Here my observations:

1) psfgen generates a different atom order for the C-terminal residue
(C-OT1-OT2 first instead of last) and for cystines where the first atom
is SG or CG for the second in the pair.
2) psfgen does not generate entries for lone pairs and charge groups.

Using psfgen outside the namd/vmd sphere can soon turn into a major
headache.