Hi,
I think the 'hbond' command in cpptraj will do what you want. It will
automatically search for all hydrogen bond donors and acceptors within
a given mask (all solute atoms if no mask given) based on the
criterion that "hydrogen bonds are FON" (i.e. hydrogen atoms bonded to
F, O, and N atoms); the total # of hydrogen bonds and some details
concerning the average behavior of hbonds over the input trajectory
can be printed. For example:
hbond out nhb.dat avgout avghb.dat
Will search for all donors and acceptors in the solute, print the # of
hydrogen bonds per frame to 'nhb.dat', and print average info to
'avghb.dat', which looks like:
HBONDS:
Acceptor DonorH Donor Frames Frac
AvgDist AvgAng
ILE_19.O THR_12.H THR_12.N 69 0.69 2.863 160.525
VAL_2.O GLU_13.H GLU_13.N 59 0.59 2.852 159.814
...
Hope this helps.
-Dan
On Tue, Nov 1, 2011 at 4:56 AM, Aditya Padhi <adi.uoh.gmail.com> wrote:
> Dear AMBER users,
> We know that from VMD we can get all the possible hydrogen
> bonds as well as its associated percentage occupancy from a MD trajectory
> file. But I want to get the distance among the donor and acceptor for all
> the H-bonds obtained from the MD trajectories. I know that the default
> distance is 3 Angstrom and angle of 20 degrees.
> If any one can help in getting the distances for every
> donor-acceptor atoms throughout the simulation I would be grateful. If any
> coding is required for this purpose or any other suggestions are there,
> kindly let me know.
>
> Thanks and regards
> Aditya.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 01 2011 - 08:00:04 PDT
