[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
amarabotti at unisa.it
Thu Jan 17 12:22:02 CET 2013
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.
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
"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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