VMD-L Mailing List

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Thu Jul 21 2005 - 12:48:58 CDT

Hi,

Use 'Patch' commands like:

patch DISU [chain name]:[residue no.] [chain name]:[residue no.]

Wei Chen

Quoting Paul R Brenner <pbrenne1_at_nd.edu>:

> 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
>
> **** From Mailing List ****
>
> From: Jim Phillips (jim_at_ks.uiuc.edu)
> Date: Mon Jan 26 2004 - 17:41:55 CST
>
> * Next message: Yusu Wang: "Re: surf for mac"
> * Previous message: John Stone: "Re: surf for mac"
> * In reply to: Han Choe: "patch in psfgen - ionic interaction and
> hydrogen
> bond"
> * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [
> attachment ]
>
> 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
> >
>
> * Next message: Yusu Wang: "Re: surf for mac"
> * Previous message: John Stone: "Re: surf for mac"
> * In reply to: Han Choe: "patch in psfgen - ionic interaction and
> hydrogen
> bond"
> * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [
> attachment ]
>
>
>
>
> 

--