Re: [AMBER] impose restraint mask for specific residues

From: Jason Swails <>
Date: Fri, 24 Jul 2015 15:30:04 -0400

> On Jul 24, 2015, at 2:09 PM, Latorraca, Naomi Rose <> wrote:
> Hi amber list,
> I'd like to run a simulation where I restrain a protein to a particular (starting) conformation and had a quick question about specifying a restraint mask for specific residues. I'm able to restrain all protein residues and heavy atoms during heating and equilibration, but I've been having trouble specifying residue selections during the production. In particular, I had been using the following to specify the restraints for certain protein residues (and not hydrogens):
> ntr=1
> restraintmask='(:65,66,132,133,136,138-142,211,214,215,217-222,225,226,229,230,291,294-298) & !.H=', restraint_wt=5.0, !hold protein fixed

This looks ok. Why do you say that the selection is wrong?

You can use ambmask to tell you the atoms that will be selected with that mask string. If the selection matches what you expected. If it does, then whatever problem exists is occurring elsewhere.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jul 24 2015 - 13:00:02 PDT
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