Re: [AMBER] request for help in water shell and closest command

From: Daniel Roe <>
Date: Tue, 31 Dec 2013 09:27:29 -0700


On Sun, Dec 29, 2013 at 11:43 PM, Robin Jain <>wrote:

> Dear amber users,
> 1. I am doing solvation of a organic molecule containing carbonyl group
> in 437 methanol. Now i want to calculate the closest 64 methanol molecule
> to my solute. I tried for this using ptraj and generate a pdb file but on
> using VMD i found that some methanol molecule are more far to solute,.what

I assume that you ran the original simulation with periodic boundary
conditions. By default cpptraj and ptraj will use the shortest imaged
distance in the 'closest' command. For visualization purposes you may want
to re-center and re-image the trajectory around your solute prior to using
the 'closest' command. In cpptraj this can be done with the 'autoimage'
command; in ptraj you need to use a combination of the 'center' and 'image'
commands. Note also that in cpptraj the 'solvent' command just uses atom
masks, so you would use something like "solvent :MOH".

> 2. An another problem is that i want to view the first and second
> solvationshell. for this purpose i used watershell command in ptraj
> and get a output
> with 3 column. what should i do further for visulization.

The 'watershell' command only gives the number of waters in the first and
second solvation shells (as defined by simple distance-based cutoffs).
Typically what you would do is take the average of each column, and use
those numbers (rounded up to the nearest integer) as input to your
'closest' commands. For example, say the average number of waters in the
first and second solvation shells ends up being 112.7 and 216.4
respectively. Your input to a 'closest' command would then be 113 and 217

Note that cpptraj has the 'outtraj' command, which allows you to run both
closest commands in the same run, like so:

closest 217 :1
outtraj netcdf
closest 113 :1
outtraj netcdf

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Tue Dec 31 2013 - 08:30:03 PST
Custom Search