RE: AMBER: Trajectory file conversion between Amber & Charmm

From: CK Sim <>
Date: Mon, 20 Sep 2004 10:45:09 -0700 (PDT)

To do analysis on Charmm trajectories, I need the Charmm topology and parameter files. I already have the these files in Amber format, therefore the question lies in how to convert these files into Charmm format. Does anyone have a clue?

Ross Walker <> wrote:
Ptraj that ships with Amber 8 should be able to do this. Although I haven't verified that it works in all cases, periodic vs non-periodic boundaries etc.
Look at page 196 of the Amber 8 manual.
Specifically you would want the following input file for ptraj (for amber to charmm):
trajin inputtrajectory.traj.gz
trajout outputtrajectory charmm
Or for charmm to amber:
trajin inputtrajectory.dcd
trajout outputtrajectory trajectory
Note, in both cases you will need a valid amber prmtop file for your molecule.
I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |


From: [] On Behalf Of CK Sim
Sent: 24 August 2004 13:42
Subject: AMBER: Trajectory file conversion between Amber & Charmm

Greetings, I am a user of both Amber and Charmm. My research work involves finding the trajectories of RNA molecules. In Amber, this information is stored in a file called *.traj which I compressed in a file format *.traj.gz. In Charmm, this information is stored in *.dcd. I use both Amber and Charmm frequently. Sometimes, the same input data is run on both Amber and Charmm because they give different information of interest. However, this takes up a lot of computer resources and processing power.

My question, therefore, is that whether there exists a way to convert .traj file formats interchangably from Amber to .dcd file formats in Charmm and vice versa. Hope you can help!

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Received on Mon Sep 20 2004 - 18:53:00 PDT
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