Hello,
The best way to learn how to use amber and its various tools (and indeed any
computational chemistry tool) is to labor through trial exercises and
documentation. That said, the exact commands are system dependent (and also
dependent on what it is you are actually trying to measure), so you should
look at the documentation and some examples to try and determine what the
commands should be for your particular system.
Look at Chapter 6, section 9 of the AmberTools manual (on my copy, it is
page 129), which discusses the hydrogen bonding utility of ptraj. There is
a tutorial on using ptraj at the Amber website
http://ambermd.org/tutorials/basic/tutorial5/ which may prove helpful.
A quick google search on how to convert gromacs trajectories to amber
trajectories suggests that VMD may be a useful tool, though I have never
done it myself.
Good luck,
Jason
On Mon, Dec 6, 2010 at 3:13 AM, leila karami <karami.leila1.gmail.com>wrote:
> Dear Jason Swails
>
> thanks for your attention.
>
> I'm beginner in using amber. please answer to my question thorough and
> exactly.
>
> what input files are necessary for hydrogen bond analysis by amber? How to
> convert gromacs file to amber files?
>
> any help will highly appreciated.
>
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Dec 06 2010 - 09:00:03 PST
