Thanks Daniel, another question came to me after reading the manual,
currently my grid calculation is center origin, if I center the trj first
and then center the grid on one specific region that I want and reduce the
box dimension instead, it will still work accurately? right?
On Sun, May 1, 2016 at 11:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sun, May 1, 2016 at 6:59 AM, maryam azimzadehirani
> <maryamai1988.gmail.com> 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?
> > http://structbio.vanderbilt.edu/archives/amber-archive/2006/2767.php
>
> 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:
> http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/
>
> -Dan
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Sun May 01 2016 - 21:00:06 PDT
