Hi,
You can convert from Amber trajectory formats to Gromacs trr with cpptraj:
trajin amber.crd
trajout gromacs.trr
However, I would like to point out that you can do hydrogen bond lifetime
analysis using cpptraj using the hbond command with the 'series' keyword,
followed by the lifetime command, e.g. to analyze solute hydrogen bond
lifetimes over 5-frame time windows:
hbond H1 series .N,H,C,O
run
runanalysis lifetime H1[solutehb] out life.5.dat window 5
See the AmberTools manual for more details. Hope this helps,
-Dan
On Sat, Mar 1, 2014 at 11:55 PM, Sohag Biswas <cy13p1001.iith.ac.in> wrote:
> dear amber users,
> I need your helps. I want to calculate hydrogen bond lifetime. For that i
> need to convert amber trajectory to gromacs trajectory. Can anybody tell me
> how to convert from amber to gromacs. It will be very helpful to me.
> Thanks.
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Mar 03 2014 - 15:30:04 PST
