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?
Choon
Ross Walker <ross.rosswalker.co.uk> 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
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
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---------------------------------
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of CK Sim
Sent: 24 August 2004 13:42
To: amber.scripps.edu
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
