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
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> AMBER.ambermd.org
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Received on Wed May 20 2009 - 12:11:10 PDT
