AMBER Archive (2002)

Subject: Re: restrain a residue as center of mass

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Nov 26 2002 - 18:17:58 CST

if you're using amber version 7, you could use targeted
MD to do this. Check the manual, it is the itgtmd=1
option in sander. What you want to do is to select using the
GROUP input the residue to restrain, and then make sure
to provide the reference coordinates for that residue. This
will allow the residue to move as a group but will restrain
it to be similar to the reference conformation. You will want
to use a target rmsd value of something close to 0.
Post again if this isn't what you want or doesn't work.
Carlos

----- Original Message -----
From: "eric hu" <erichu_linux_at_yahoo.com>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, November 26, 2002 6:36 PM
Subject: restrain a residue as center of mass

> Hi, I want to freeze the internal motion of an
> unnatural residue which happens to have two molecules.
> I still want the residue's center of mass to have all
> the freedoms. I wonder if there is way to do this. I
> have tried to constrain individual atoms or bond
> distances and they will either fix the atoms in the
> space of there are still internal motions. Thanks a
> lot.
>
> Regards,
> -Eric
>
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