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

[Oliver Grant]

I suppose it depends on what kind of analysis you would like to do... I'm
not aware of any scripts for converting back from gmx into amber
trajectories but I have done this before when doing an mmpbsa calculation
using ambertools. As I only needed "snaphots" of the trajectory and not
energies or velocities I used trajconv to write out pdb's for each timeframe
I wanted then used a script to change the pdb's so that the atom names were
compatible with amber. I then used ptraj to merge them into one crd file.
Each case requires special attention though and it is cumbersome and time
consuming. If you really need to do this I can share the script with you but
I strongly recommend you either find a way to do the analysis with gmx or
re-run the simulation with amber.

Oliver

On 7 December 2010 07:08, leila karami <karami.leila1 at gmail.com> wrote:

> Dear gromacs users
>
> I did simulation of protein-dna by gromacs and amber03 force field. I want
> to do some analysis by amber. what is the best way for conversion of gromacs
> trajectory and topology files 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
>
>
>
> --
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