RE: AMBER: Trajectory file conversion between Amber & Charmm

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 24 Aug 2004 16:51:17 -0700

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
 
/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |


 


  _____

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 Wed Aug 25 2004 - 00:53:01 PDT
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