On Sun, May 1, 2016 at 9:55 PM, maryam azimzadehirani
<maryamai1988.gmail.com> wrote:
> 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?
I'm not sure I understand what you mean. It's best if you post the
exact commands you use/want to use.
I think you mean you want to center the grid on the origin, then
center a certain region of interest on the origin as well? That should
work fine. Your best bet though is to try it out on a limited number
of frames (something you can run quickly) and make sure the output
looks like what you would expect.
Hope this helps,
-Dan
>
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
-------------------------
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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Received on Mon May 02 2016 - 08:00:04 PDT
