VMD-L Mailing List

From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Mon Jun 09 2014 - 07:28:40 CDT

Dear Revathi,
                   Try the following commands.
                   pbc unwrap -all
                   pbc readxst file.xst -stride 10 (what ever you load)
                   pbc join residue -first first -last last
                   pbc wrap -centersel "protein" -center com -compound
residue -all

Cheers,
Subbarao Kanchi.

On Mon, Jun 9, 2014 at 5:01 PM, Revthi Sanker <revthi.sanker1990_at_gmail.com>
wrote:

> 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
> -------------------------------------------------------
>
>