Re: [AMBER] Specifying disulfide bonds in a protein model

From: Anselm Horn <Anselm.Horn.biochem.uni-erlangen.de>
Date: Thu, 21 Jun 2012 12:45:22 +0200

Hi John,

maybe your residue numbering is the problem:
When you load a pdb into leap, all residues are renumbered consecutively
starting with 1. Hence, you cannot use the original pdb residue numbers
in most cases.

A simple check would be to load the pdb into leap, omit the CYX-CYX-bond
command and save the system in crd/top (to check that everything else is
ok) and pdb format.
Then you use this pdb file with the new residue numbers as input of a
second leap-invocation where you add the cystine bond.

Regards,

Anselm

Bioinformatik
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany

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Received on Thu Jun 21 2012 - 04:00:02 PDT
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