RE: AMBER: restraints to individual atoms

From: Ross Walker <>
Date: Tue, 27 Nov 2007 09:05:44 -0800

Hi Eddie,

> restraintmask=':541,542,543'
> I would like however, to make a restrain on atoms within the
> specified
> restraintmask residues,
> I know that for the qm/mm region it is possible to pick
> atoms instead of
> residues, but what
> about the restraintmask section?.

You can pick individual atoms in the mask using the .symbol. So for example:

restraintmask=':5-7 | .121-124,155,157',

Would select atoms that were either part of residues 5,6,7 OR were atom
numbers 121,122,123,124,155,157.

I believe that this is not an exclusive or and so you can have atom numbers
that overlap with the residue selections. Although I haven't tested this.
For a full description of the ambmask language see page 287-288 of the Amber
9 manual.

Good luck,


|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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Received on Wed Nov 28 2007 - 06:07:37 PST
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