On Mon, Apr 7, 2014 at 5:52 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Mon, Apr 07, 2014, Neha Gandhi wrote:
>>
>> I might be ignorant about NMR observables. Can you please guide me if there
>> is a way to calculate (1/r^6)¨(-1/6), which is the NMR averaged distance
>> from the trajectory? My MD runs are in presence of explicit solvent without
>> any restraints.
>
> I think you need to use the "distance" command in cpptraj, then post-process
> this with your own script to get the average you want. This might eventually
> become an option for the "type noe" option for "distance", but that is not
> there now.
Dave is right. This capability is not currently there, but will be
available (soon) in cpptraj from the upcoming Amber 14 release via the
'statistics' analysis command for distances labeled with 'type noe'.
-Dan
--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Apr 07 2014 - 08:00:03 PDT
