Re: [AMBER] Reading NetCDF file

From: Daniel Roe <>
Date: Fri, 4 Oct 2013 08:05:46 -0600


On Fri, Oct 4, 2013 at 6:46 AM, Uday Midya <> wrote:
> I have tried to read a dcd file generated from the mdcrd file by ptraj
> module. The code that I used works fine with the NAMD generated dcd file.
> But it fails to read the ptraj generated one.

Can you describe how it fails in a little more detail (coordinates are
garbled, box information is wrong etc)? If you can give more specific
details we may be able to help more. Also, do DCD files generated with
cpptraj have the same issues for you?

> Can any one give me a fortran code or some tips for the reading of amber12
> binary trajectory file or the ptraj generated dcd file with/without box
> information.

As far as I know there is no Fortran code in Amber that reads/writes
DCD files. For examples in C/C++ you can see what happens under the
hood in ptraj in trajectory.c (functions readCharmmTrajectory() and
dumpCharmmTrajectory()) or in cpptraj in Traj_CharmmDcd.cpp.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Fri Oct 04 2013 - 07:30:09 PDT
Custom Search