VMD-L Mailing List

From: Revthi Sanker (revthi.sanker1990_at_gmail.com)
Date: Mon Jun 09 2014 - 06:31:11 CDT

Dear all,
I am trying to use pbctools to wrap and recenter my protein. The steps
used are:

pbc unwrap
pbc set {142 142 142} -first now -all
pbc wrap -centersel "protein" -center com -compound residue -all

But the output is a structure with a lot of wrong contacts. I am unable to
rectify the error. Is the set of commands I am using, right?

Kindly provide your valuable suggestions.

Thank you in advance.

Revathi.S
M.S. Research Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute Of Technology, Madras
India
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