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 <[email protected]> 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 > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
