AMBER Archive (2003)

Subject: Re: Groups defenition

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 09 2003 - 10:59:11 CDT

On Tue, Apr 08, 2003, Javier Cuervo wrote:
>
> There is a easy way to put in a group the residues of an interface between
> to proteins?
>
> The problem is that this residues are not contiguos in the secuence, and
> it seems to me I have to specify explicitly ALL the residues in the
> interface in one group, and again explictly every other residue that does
> not belong to the interface in a second group.

I'm not sure whether you are talking about groups in mm_pbsa or in sander.
For the latter, there may be no "easy" way, but it's not that hard either:

RES 5 10
RES 12 12
RES 14 14
RES 161 163
...

will add the requested residues to the group. You can have as many RES cards
as you need.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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