AMBER Archive (2009)

Subject: Re: [AMBER] multiple chain specification in Sander

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 07 2009 - 05:19:09 CDT

there is no chain designation in amber. all residues are numbered consecutively.
if you load your prmtop and coordinates into VMD you can check residue
numbers and use those.

On Wed, May 6, 2009 at 11:17 PM, Siddharth Rastogi
<siddharthrastogi08_at_gmail.com> wrote:
> Dear AMBER users,
>
> I have a simple query.  In my protein of interest, there exists two chains
> with same number of amino acid residues.
> I want to restrain few residues from chain A and few others from chain B.
> Can anybody help me, what symbol will be used to specify each chain and
> residues in a sander input file ?
>
> I was going like : 1-50.A_at_CA,C
>
> But sander replies back as:
>
> *Error in group input::atommask.f::residue_namelist
> residue name should not have more than 4 chars*
>
> Can anybody help me in this regard.
>
> Thanks in advance.
>
> Siddharth
>
> --
> Siddharth Rastogi
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