VMD-L Mailing List

From: Paul R Brenner (pbrenne1_at_nd.edu)
Date: Thu Jul 21 2005 - 13:26:53 CDT

Thanks for the responses. I now understand better the utility of patch as given
in the psfgen user's guide and where the DISU patch is defined in the topology
file. I notice that Chris's DISU patch differs from the top_all22_prot.inp
patch.

Chris,

Was there any particular reason for your formulation of the DISU patch?

Thanks,
Paul

Quoting "Chang, Christopher" <Christopher_Chang_at_nrel.gov>:

> Paul,
>
> During the build, you have to apply a patch to establish the bond between
> the cysteines. The example I have is
> ------------------------------------------------
>
> PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS.
> GROUP ! use in a patch statement
> ATOM 1CB CT2 -0.10 !
> ATOM 1SG SM -0.08 ! 2SG--2CB--
> GROUP ! /
> ATOM 2SG SM -0.08 ! -1CB--1SG
> ATOM 2CB CT2 -0.10 !
> DELETE ATOM 1HG1
> DELETE ATOM 2HG1
> BOND 1SG 2SG
> ANGLE 1CB 1SG 2SG 1SG 2SG 2CB
> DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG
> DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG
> DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA
> DIHE 1CB 1SG 2SG 2CB
> !DIHE 1CB 1SG 2SG 2CB
> IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000
> IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
> -----------------------------------------------------------------
>
> This goes in your topology file. In the build script, it's applied as
> -------------------------
> patch DISU SEG1:X SEG2:Y
> -------------------------
>
> where SEG1 is the segment containing one of the cysteines, SEG2 is the
> segment containing the other, X is the residue number of the first cys, and Y
> is that for the second. The first residue specified after "DISU" will be "1"
> in the patch, the second "2". They can be in the same segment, in which case
> SEG1=SEG2. Ignore the lines of dashes, they're just here for clarity.
>
> Hope that helps,
>
> Chris
>
> Christopher H. Chang, Ph.D.
> Research Associate
> National Renewable Energy Laboratory
> 1617 Cole Blvd., Mail Stop 1608
> Golden, CO 80401
> Phone (303) 275-3751
> Fax (303) 275-4007
>
>
>
> > -----Original Message-----
> > From: owner-vmd-l_at_ks.uiuc.edu
> > [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf
> > Of Paul R Brenner
> > Sent: Thursday, July 21, 2005 10:16 AM
> > To: vmd-l_at_ks.uiuc.edu
> > Subject: vmd-l: Representing disulfide bonds when using psfgen
> >
> >
> > 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 ]
> >
> >
> >
> >
> >
>