AMBER Archive (2002)

Subject: Re: disulfide bond link between two chains

From: Natasja Brooijmans (nbrooij_at_itsa.ucsf.edu)
Date: Mon Dec 16 2002 - 07:49:46 CST

Leap "renumbers" atoms based on chains. The first chain will have the
regualr residue numbers, the second chain will have residue numbers +
10000, third chain res # + 20000. SO in your case it would be 10201.

Natasja Brooijmans
Graduate Program in Chemistry & Chemical Biology
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-0446
phone: 415-476 8291
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu

On Mon, 16 Dec 2002, pu xuemei wrote:

> Hello
> I am dealing with one structure containing three chains. There is no
> problem when I link disulfide within the first chain in xleap, using "bond"
> command. but there is error information as follows when I link disulfide
> between the first chain and the second chain using same command
> >bond cam.132.SG cam.201.SG
> bond: Argument #2 is type string must be of type:[atom]
> using: bond <atom1> <atom2> [order]
> (132 from the first chain and 201 from the second chain)
> Furthermore, when I use "desc" command to view the information about
> residue 201, there is no information
> >desc cam.201
> 'cam.201'
> I guess that xleap couldn't find the SG atom in res 201,even res 201. but I
> don't know how to deal with the problem. Could anybody help me. Thanks in
> advance.
> Best regards!
>
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