VMD-L Mailing List
From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Thu Jul 21 2005 - 12:39:06 CDT
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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 ]
>
>
>
>
>
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