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
