[AMBER] Exceed character limit in bellyrestraint mask selection

From: Mike Limb <mikeallimb.gmail.com>
Date: Tue, 15 Oct 2013 16:29:18 +0100

Dear AMBER users,

I am setting up a QM/MM optimisation for a protein ligand system with
explicit solvent.

My QM region consists of 50 atoms (a ligand and two residue side chains)
and the rest of the system is treated with MM.

Within the MM region I would like to fix the positions of all the atoms of
any residues that are not within 10 A of the QM region. To do this I would
like to use the ibelly restraint. However, the problem arises here, as the
most economically way I can think to specify the moving atoms (using
residue numbers) in the bellyrestraint selection mask, still far exceeds
the 256 character limit imposed for the mask selection.

I have thought about trying to rename all the residues I want to select as
a separate residue number however,I believe, this would result in errors
when generating a topology file.

Looking through the mailing list archive I saw one solution purposed for a
user with a similar problem where she was instead limited by a restraint
mask limit was :

"Use the "old style" restraints, i.e. using the group syntax, without the

but I don't understand what is meant by "using the group syntax, without
the restraintmask" and whether it is a viable solution to my problem!

Any advice or help would be appreciated (please find attached a file
containing a the residue selection required),

Many thanks,


Mike Limb
PhD Candidate
SCI Scholar 2013-2016        *http://www.soci.org*
Supervisor: Prof. Adrian Mulholland
Centre for Computational Chemistry
School of Chemistry
University of Bristol
Bristol BS8 1TS
Post-Graduate Research Senate Representative at UoB
Post-Graduate Research Representative University Graduate Studies Committee
at UoB
Broadcast Assistant BBC Introducing in the West at BBC Radio Bristol
Executive Producer of Burst Student Show at BCFM

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Received on Tue Oct 15 2013 - 08:30:02 PDT
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