[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format

Anna Marabotti amarabotti at unisa.it
Thu Jan 17 12:22:02 CET 2013

Dear all,
we'd need to convert a trajectory in .xtc format (and the related 
topology file) to a format that could be read by Amber program (I'd need 
to perform MM-PBSA calculations).
We tried to do it using VMD, but failed to produce a correct trajectory 
to be read by MMPBSA.py tool. It complains about the fact that it 
expected only 3 or 6 box coords, but I ran the trajectory using a 
rhombic dodecahedric box, with 9 box coords.
I read the gmx-user archive to find hints to overcome the problem, but 
only found incomplete, and in some cases quite old, suggestions (We are 
currently using Gromacs 4.5.4 version). I don't see anywhere a detailed 
suggestion on how to proceed, and I have even the doubt that this is not 
possible to do.
Could you please give me some information about, possibly with detailed 
descriptions about the commands and the flags to use?

Many thanks in advance for your kind answer and best regards

Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabotti at unisa.it
Skype: annam1972

"When a man with a gun meets a man with a pen, the man with the gun is a dead man"
(Roberto Benigni, about Roberto Saviano)

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