[gmx-users] conversion of gromacs files to amber files

[Oliver Grant]

Hi Leila,

I've done this with g_hbond and g_bond. If you search the forums there is a
perl script available from Justin Lemakul that will do this for you. You can
do it manually too if you have only a few to look at. Its a little tricky
but a lot easier than traj conversion. :) I was able to get % residence,
average bond length and std dev of length but I had to use ndx files with
just the 3 atoms in them. It's tedious so if you have a lot of bonds check
out the perl script.

Oliver

On 7 December 2010 10:56, leila karami <karami.leila1 at gmail.com> wrote:

> Dear Oliver Grant
>
> thanks for your attention.
>
> I want to use amber tool for hydrogen bond analysis especially (water
> mediated hydrogen bonds and residence time and occupation of them).
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
>
>
>
> --
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