VMD-L Mailing List

From: Paul R Brenner (pbrenne1_at_nd.edu)
Date: Thu Jul 21 2005 - 11:15:30 CDT

I looked through the mailing list and user's guide but found only one mention of
psfgen and disulfide bonds (included at the end of this email). I am trying to
use psfgen to generate a psf for BPTI (5pti pdb) which has three primary
disulfide bonds. When I image the pdb, VMD accurately guesses the existence of
the bonds but when I generate the psf with psfgen the sulfur bonds are deleted.
Does anyone have experience accurately representing disulfide bonds when using
psfgen? I have tried both the top_all22_prot.inp and top_all27_prot_lipid.rtf
files.

Thanks,
Paul R Brenner

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From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Jan 26 2004 - 17:41:55 CST

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    * In reply to: Han Choe: "patch in psfgen - ionic interaction and hydrogen
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Hi,

Ionic and H-bond interactions has are represented by a combination of
electrostatic and Lennard-Jones (vdW) terms in the force field, and even
if there were special terms they would not apply to specific combinations
of atoms or residues as a disulphide bond does. Therefore there is no
patch needed to add them explicitly to a system.

-Jim

On Mon, 26 Jan 2004, Han Choe wrote:

> Hi everyone,
>
> Is it possible to patch ionic interaction and hydrogen bond like
> disulfide bond during generation of a psf file?
>
> Cheers,
> Han
>

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    * In reply to: Han Choe: "patch in psfgen - ionic interaction and hydrogen
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