AMBER Archive (2004)

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

From: Austin B. Yongye (ayongye_at_sunchem.chem.uga.edu)
Date: Thu Jul 29 2004 - 08:13:46 CDT

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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Dr. Woods' Research Group
University of Georgia
Complex Carbohydrate Research Centre
315 Riverbend Road
Athens, GA 30602

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