Re: [AMBER] MASK with distance in AMBER.

From: Daniel Roe <>
Date: Fri, 12 Aug 2016 11:54:05 -0600


Most of this information is in the Amber 16 manual, in 29.2.2 "Atom
Mask Selection Syntax" under "Distance-based Masks". In particular:

"Distance-based masks that update each frame are currently only
supported by the mask action."

Also, the 'mask' command doesn't affect subsequent commands. The
reason for this is that it is likely with distance based masks that
you will be selecting different numbers of molecules for each frame,
which would require that actions essentially be re-setup for a new
topology each frame, which is both expensive and impractical.

In your case you probably want to estimate the average number of
molecules within 6.0 Angstroms of residues 1-1158 (using e.g.
'watershell' with an increased second (upper) shell distance cutoff),
then use the 'closest' command to retain exactly that number of water

Hope this helps,


On Fri, Aug 12, 2016 at 9:48 AM, Parviz Seifpanahi Shabane
<> wrote:
> Hi All,
> I need to use the mask command with distance for my job (below). as you
> know for using the mask with the distance we need to give the reference to
> Cpptraj. I need to know, how to Cpptraj work on this situation?
> My impression is that Cpptraj uses the reference for finding the molecules
> (in my case water) in the special distance which was defined by the mask
> from the reference file and then track those molecules down during the
> simulation, is that correct?(number of molecules did not change for my
> case)
> does the Cpptraj update the molecules for each frame?
> it could be the bug for Cpptraj because molecules will move during the
> simulation and too many of properties (in my case auto-correlation function
> of the dipole of water molecules near the protein) depend on the position
> of molecules.
> parm
> reference 3v03-H++-2braanch.prod1.restrt
> trajin 3v03-H++-2braanch.prod2.traj
> mask (:1-1158<:6.0)&:WAT
> vector v0 dipole out dipole-G6A.dat (:1-1158<:6.0)&:WAT
> timecorr vec1 v0 out auto-correlation-function-G6A.dat order 1
> Best Regards
> Parviz
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Aug 12 2016 - 11:00:04 PDT
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