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. <br>
<br>Oliver<br><br><div class="gmail_quote">On 7 December 2010 07:08, leila karami <span dir="ltr"><<a href="mailto:karami.leila1@gmail.com">karami.leila1@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear gromacs users<br><br>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?<br>
<br>any help will highly appreciated.<br clear="all"><font color="#888888"><br>-- <br><pre style="font-family: arial,helvetica,sans-serif;">Leila Karami<br>Ph.D. student of Physical Chemistry<br>K.N. Toosi University of Technology<br>
Theoretical Physical Chemistry Group</pre>
<br>
</font><br>--<br>
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