On Tue, May 3, 2016 at 6:00 AM, maryam azimzadehirani
<maryamai1988.gmail.com> wrote:
> this is my cpptraj output file for one residue:
> I am not sure what does count and frac columns present? first thought count
> should be number of frames that we see this Hbond, but for some residues I
> get the count number larger than my total number of frames. does this means
> there is something wrong with my analysis?
The Amber manual explains this (section 29.9.34 hbond, page 589):
"Count is the total number of interactions between solute and solvent
(note this can be greater than the total number of frames since for
any given frame more than one solvent molecule can hydrogen bond to
the same place on solute and vice versa),"
Make sure you read the manual entry for the 'hbond' command carefully.
Hope this helps,
-Dan
>
> #Solute-Solvent Hbonds:
> #Acceptor DonorH Donor Count Frac
> AvgDist AvgAng
> SER_11.O SolventH SolventDnr 112 1.1200
> 2.7462 158.7748
> SolventAcc SER_11.HG SER_11.OG 77 0.7700
> 2.7717 161.6080
> SER_11.OG SolventH SolventDnr 66 0.6600
> 2.8063 159.1450
> SolventAcc SER_11.H SER_11.N 42 0.4200
> 2.8861 159.3242
>
> Regards,
> Maryam
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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 Tue May 03 2016 - 07:00:05 PDT
