Re: [AMBER] Exceed character limit in bellyrestraint mask selection

From: Jason Swails <>
Date: Fri, 18 Oct 2013 14:05:47 -0400

On Fri, Oct 18, 2013 at 1:35 PM, Mike Limb <> wrote:

> Dear Jason,
> Many thanks for your useful reply.
> I found a mask specification that allowed me to freeze all the atoms I
> wanted. This was done with the command:
> bellymask=(!.1962-1998,541-547,778-783 < :10.0)

bellymask selects atoms that can move, not atoms that are fixed. This will
fix all residues within 10 angstroms of your atom selection and allow
everything else to move. I don't think this is what you want, right?

> this command allows me to freeze all residues that are within 10 A of the
> QM region (which consists of atoms 1962-1998,541-547,778-783 ).
> With this setup I then performed a two dimensional QM MM scan (adiabatic
> mapping) with an x_series consisting of a distance restraint (between atom
> 782 to 1991) from 1.4 to 3.3 A and y_series consisting of a distance
> restraint (1991 to 1993) from 4.1 to 1.4 A, thus generating a potential
> energy surface.
> On analysis of the results I noticed that there were large discontinuities
> in the energies that I had calculated.
> Inspection of my output files revealed that this was most likely due to the
> fact that the region that fell within the belly mask restraint moved as the
> size of the QM region changed during the reaction. As a result I was
> getting inconsistencies in the size of my MM region (and frozen region) as
> the scan progressed and hence jumps in the total energy.
> I though that one way to solve this problem could be to use the positional
> restraints with the restraint mask:
> restraintmask=':* & (!.1962-1998,541-547,778-783 < :10.0)',

The :* is redundant here.

> and then using a refc structure, however, upon testing it seems that the
> atoms that are included in the restraint are still selected using the
> coordinate file that is read in at the beginning of the optimisation and
> therefore the same problem of a changing frozen region still remains.

> Consequently, I believe my only option left it to use the Group selection
> detailed in Appendix B. Upon attempting this I don't understand the
> documentation or the example that is given and how I can use the group
> selection to allow me to select the residues that I would like to fix in my
> optimisations (a list of which are attached).
> As a result I was wondering if you could give me some guidance how I could
> do a setup of this type.
> eg say I had a ligand (resid 1) and surrounded by a two solvation layers of
> water the first consisting of residues 2-10 and the second consisting of
> 11-30.
> How could I use the group selection to tell sander during the optimisation
> to do a QM optimisation of the ligand, MM on the rest of the system, *BUT
> freezing the coordinates of the second solvation shell by specifying them
> by the residue number using the group selection. *

Your QM region should be specified the same way (i.e., with atom numbers or
a mask). To fix residues 11 through 30 using belly and the GROUP input, it
would look something like this:

   ...your variables here...
Movable atoms
RES 2 10

This will allow residues 2 through 10 to move. You can alternatively
specify atom numbers and ranges using "ATOM" instead of "RES". You can
specify at most 7 residue or atom ranges per line, but can specify as many
lines as you want. Also, you must specify _ranges_. If you want just 1
residue, you need to specify it as a range (e.g., "RES 1 1").

Another example:

   ... your variables here...
Movable atoms
RES 1 10 20 30 35 35 37 37 39 39 50 58 60 72
RES 80 80 82 82 84 84 86 86 88 88 90 90 92 92

The above will allow residues 1 through 10, 20 through 30, 35, 47, 49, 50
through 58, 60 through 72, 80, 82, 84, 86, 88, 90, and 92 to move. I don't
know if there is a limit to how many lines you can specify, but I don't
think there is.

Keep in mind, belly selections and restraint selections are inverse
compared to each other. Belly selections indicate atoms that can move
while restraint selections indicate atoms that are restrained.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 18 2013 - 11:30:03 PDT
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