[AMBER] impose restraint mask for specific residues

From: Latorraca, Naomi Rose <nlatorra.stanford.edu>
Date: Fri, 24 Jul 2015 18:09:02 +0000

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):


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

and I also specify the -ref file in my submission script. Is there something wrong with my syntax or how I'm trying to implement positional restraints in general?

Thanks so much in advance!


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Received on Fri Jul 24 2015 - 11:30:02 PDT
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