Re: [AMBER] Regarding population of hydrogen bond

From: Wesley Michael Botello-Smith <>
Date: Wed, 13 Feb 2019 11:24:31 -0800

I believe you can get the needed data with the 'series' flag and
corresponding uuseries or uvseries files. I have used this for classifying
hbond interactions between solute and membrane headgroups before although
I'm not sure how easy it will be for water-water since there doesn't seem
to be a solvent-solvent series flag directly available so you may have to
do a bit of leg work to get cpptraj to print out a series for that.

For example, using:
hbond out test_hb.out.dat :1,WAT solventdonor :WAT solventacceptor :WAT
series uuseries test_hb.uuseries.dat uvseries test_hb.uvseries.dat
on a small protein trajectory I have on hand yields uvseries:
#Frame GLU_1.OY-V GLU_1.HN-V GLU_1.OE2-V GLU_1.OE1-V GLU_1.O-V
       1 2 1 3 4 1
       2 1 0 3 3 0
       3 1 0 4 2 2
       4 2 1 3 2 1
       5 2 1 3 4 2

So this gives the total hbond contacts between each site on GLU1 and any
nearby :WAT sites. So for solvet-solute this is everything you would need
(with a bit of fenagling in R, python, etc to frame-wise aggregate over
each solute). Unfortunately, I'm not sure how you could get an equivalent
output for solvent-solvent. The resulting file could easily be quite
enormous since each water would occupy 4 columns ( two donor sites and two
acceptor sites each). E.g. if you had ten thousand water atoms, the maximum
potential memory usage becomes bounded as storage of a 40000 x 40000 x
nFrames array... that could take hundreds of terabytes worth of memory.
Assuming you can do so, however, you could frame-wise sum over all four
hbond sites for each water molecule to yield the total number of hbonds for
each individual water molecule at each frame.

On Tue, Feb 12, 2019 at 5:26 PM MOHD HOMAIDUR RAHMAN <>

> Dear AMBER user's
> I want to calculate the population of water-water hydrogen bond forming in
> my water simulation. For example, in my simulation box, I have a total of
> 1000 water molecules. Now I want to calculate the percentage of water
> molecules forming only one or two or three or four hydrogen in a box.
> As I know, cpptraj only print average H-bond. It is possible to print
> population of hbond.
> Kindly guide me, thank you in advance.
> Regards
> Rahman
> '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
> *M*d* H*omaidur* R**ahman *( Research Scholar )
> Lab No. 510, Computational Biophysics Lab.
> Department of Biotechnology
> Indian Institute of Technology-Madras
> Chennai-600 036, India
> *Mobile No = +91- 7845991785*
> '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Wed Feb 13 2019 - 11:30:02 PST
Custom Search