Thank you
Best Regards,
*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
On Sun, Jan 3, 2016 at 8:31 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, Jan 3, 2016 at 3:40 AM, neha chaudhary <nehachaudhary769.gmail.com
> >
> wrote:
>
> > Dear Sir/Ma'am,
> >
> > I have done MD simulations in Gromacs earlier, now I want to convert
> output
> > trajectory file into Amber format (.dcd). I don't know how to do it.
> > Please help.
> >
>
> cpptraj can do this on the command-line. You can do it something like
>
> cpptraj -p <parm> -y <gromacs_trajectory> -x converted_trajectory.dcd
>
> Here, <parm> can be any Amber topology file or, if you are using GROMACS,
> a PDB file (which is usually the precursor to a GRO file). If you don't
> have PDB file, you can use pdb2gmx to convert a .gro file to a .pdb using
> something like (for GROMACS version 5+):
>
> gmx pdb2gmx -f your_file.gro -o your_file.pdb
>
> I think... I don't use GROMACS often. Once you have your PDB file,
> cpptraj can use that as a topology. Another option is to use the
> "mdconvert" program from the MDTraj package, which supports GRO files
> directly. That can do all of the conversions you need as well.
>
> One comment I will make, though, is that DCD is *not* an Amber-format
> trajectory. Amber uses NetCDF or plain ASCII for its trajectory formats.
> DCD files originated with CHARMM, although it is used by several different
> programs as its principal trajectory format (e.g., NAMD).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Jan 03 2016 - 21:30:03 PST
