AMBER Archive (2004)

Subject: Re: AMBER: tleap: automatically identify and connect disulfide bonds?

From: Raik Grünberg (graik_at_web.de)
Date: Mon Aug 02 2004 - 04:15:34 CDT

Hi Austin, sorry about the late response,

My question was more whether the process of actually identifying atoms that
should form S-S bonds can be put into a ptraj script. And there the answer
(according to Scott) is yet No. Anyway, I've got some python code that is
already doing that and it's not a big deal to write a little python script
that is generating a ptraj script.. Thanks for your response, next time I'll
try to be more specific with the question.

Raik

On Thursday 29 July 2004 15:13, Austin B. Yongye wrote:
> You can write a short script that loads the pdb file, adds hydrogen atoms
> (if it's a crystal structure), reload the new pdb file, and link the
> cysteine residues
> 1. In pdb file (cyrstal structure), change the CYS residues involved in
> the disulphide bonds, to CYX (call this file eg first.pdb)
> 2. Write short script:
> #script
> source <amber_force_field>
> abc = loadpdb first.pdb
> savepdb abc first_with_hydrogens.pdb
> xyz = loadpdb first_with_hydrogens.pdb
> #atoms involved in disulphide bridge
> bond xyz.<first_residue_number>.SG xyz.<second_residue_number>.SG
>
> If your pdb already has hydrogens(not a downloaded crystal structure), do
> step 1, and use this script:
> #script
> source <amber_force_field>
> xyz = loadpdb first_with_hydrogens.pdb
> #atoms involved in disulphide bridge
> bond xyz.<first_residue_number>.SG xyz.<second_residue_number>.SG
>
> Repeat the "bond" command for all the disulphides you wish to create.
> Page 45/53 of AMBER 7/8 will also be helpful.
>
> > Hi,
> >
> > On Wed, 28 Jul 2004, Raik [iso-8859-1] Grünberg wrote:
> >> is there a way to make tleap identify and connect disulfide bonds
> >> automatically? The bondByDistance <container> command looks like it
> >> could be
> >> used for that but I don't see how to specify a container that contains
> >> only
> >> the SG atoms of a molecule. The manual doesn't seem to tell what a
> >> container
> >> is and how it can be specified.
> >
> > Not yet, but I shall be looking into it.
> > I do not believe that bondByDistance can be used to connect disulfide
> > bonds.
> > See page 48 of the Amber8 manual for the canonical disulfide procedure.
> >
> > Scott
> >
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