Re: [AMBER] Gromacs to Amber trajectory

From: Lorenzo Gontrani <>
Date: Thu, 16 Jun 2011 18:10:06 +0200

Dear Raja, I use VMD to convert the Gromacs trajectory into dcd
format, and then use ptraj to read the dcd file and write the mdcrd
(or AMBER netcdf) trajectory. It's one of the possible ways, and it
works fine to me.
Always remember to save a structure file (PDB, GRO).
You could also prepare an ASCII trajectory of PDB files, or XYZ files.
The problem, in those cases, are the box dimensions (for NPT



2011/6/16 Raja Pandian <>:
> Dear All,
> I have created Amber input file (.prmtop and .rst7) using Xleap. And then I
> have converted this input file into Gromacs input file format (*.gro and
> *.top) with script. I did simulation using Gromacs Package (Amber
> Force Field). Now I would like to convert Gromacs trajectory file to Amber
> trajectory file format. So that I can easily analyses this trajectory. I
> tried to convert Gromacs trajectory file to Amber trajectory file using VMD.
> This VMD converted trajectory is not working fine. Pls help me in this
> regards
> Eagerly waiting for your suggestion.
> Regards
> Raja
> _______________________________________________
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 Lorenzo Gontrani
 Research associate of EDXD group
 University of Rome "La Sapienza"
 GSM +39 338 7615798
 Email l DOT gontrani AT caspur DOT it
 Webpage: http://webcaminiti/gontrani.html
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Received on Thu Jun 16 2011 - 09:30:03 PDT
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