Re: [AMBER] Convert gromacs output file to Amber format

From: Jason Swails <>
Date: Sun, 3 Jan 2016 10:01:12 -0500

On Sun, Jan 3, 2016 at 3:40 AM, neha chaudhary <>

> 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).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Jan 03 2016 - 07:30:04 PST
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