Re: [AMBER] water residence time calculation

From: Daniel Roe <>
Date: Sun, 1 May 2016 09:42:20 -0600


On Sun, May 1, 2016 at 6:59 AM, maryam azimzadehirani
<> wrote:
> Dear Amber users,
> I have used ptraj grid command to calculate the water densities of two
> system. However to interpret my density maps I need to know the residence
> time of waters around some specific residues. I have found this question in
> the mailing list. but there is not a solution to it. can you tell me how to
> do this analysis?

There actually is a solution listed there - use the 'hbond' command,
though I recommend using cpptraj instead of ptraj. You'll probably
want to also use the 'lifetime' analysis command. See the manual for
details on the commands as well as examples. This tutorial may also
provide some insight:


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)
AMBER mailing list
Received on Sun May 01 2016 - 09:00:04 PDT
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