AMBER Archive (2009)

Subject: Re: [AMBER] Disulfide bond

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Tue Apr 21 2009 - 20:46:19 CDT

Hi,

       Sleap has the functionality to create disulfide bond
automatically.
You can enable this function by add:

     set default disulfide auto

to your leaprc.

     What sleap does is it calculates the distance between two sulfur
atoms
if the distance < disulfcut, a disulfide bond will be created and the
residue
name will be changed accordingly.

    About the value "disulfcut", by default it is 2.1. it can be
changed by

     set default disulfcut x.xx

    There is an example showing how to do this in directory:

     amber10/test/sleap/disulfide/Run.auto.H

     Sincerely,

     Wei

On Apr 21, 2009, at 8:37 PM, Dong Xu wrote:

> Hi,
>
> Is there a way to automatically identify the CYX residues and bond
> them in Leap?
>
> I found that sometimes it takes numerous trials to locate the
> correct CYX residue number for leap when there are additions in PDB
> files. It'd be nice to have a smart and automated way of doing that.
>
> Thanks!
>
> Dong Xu
> UC, San Diego
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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