Re: [AMBER] saving the first solvent shell molecules by Ptraj

From: Daniel Roe <>
Date: Tue, 28 Jun 2011 00:41:55 -0400


On Mon, Jun 27, 2011 at 8:24 AM, Zhu Tong <> wrote:
> However, when I check the output structure by VMD, I found there are a
> lot of waters which are far very far from the solute. Could you tell me
> where I have slipped up ?

The closestwaters command uses imaged distances to decide what is
close to the mask you specify, so I suspect what you are seeing is an
artifact of the periodicity of the system. What you can do is during
the first pass when you are determining the number of waters in the
1st and 2nd solvation shells, center the coords on your solute and
reimage, like:

trajin prod.mdcrd 1 1000 200
watershell :1-76 test.out lower 4.0
center :1-76
image origin center

Then in your second step when you are calculating the closest waters
use the '' trajectory. Let me know if you have
any more questions.


AMBER mailing list
Received on Mon Jun 27 2011 - 22:00:03 PDT
Custom Search