Re: [AMBER] Generating topology files for two proteins in a single input pdb

From: David A Case <>
Date: Tue, 1 Oct 2013 07:43:07 -0400

On Mon, Sep 30, 2013, George Green wrote:

> cat mou_stage1.pdb hum_stage1.pdb > mou-hum_stage2.pdb
> grep -v END mou-hum_stage2.pdb > temp
> mv -f temp mou-hum_stage2.pdb

Make sure that the final pdb file actually is correct (i.e. examine it in a
text editor).

> If there are two proteins in the same amber topology file is there any way
> (i.e. some label) to distinguish between the two apart from residue number?

No. The amber atom selections and other analysis tools don't have any notion
of a chain or stand number. (Our excuse: they were adapted from Midas and
Chimera). I have some thoughts about how we could do this in a reasonably
simple way, but it would still be a fair amount of work.


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Received on Tue Oct 01 2013 - 05:00:09 PDT
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