Re: AMBER: convert_trajectory

From: Thomas E. Cheatham, III <>
Date: Wed, 27 Jul 2005 17:45:34 -0600 (Mountain Daylight Time)

> I change a little bit to make PSF recognized. But ptraj dumps
> one more residue at the beginning of AA sequences. Actually,
> it duplicates the first residue. Why does this happen?

Based on the information given, I have absolutely no idea. Unless ptraj
is misinterpreting the PSF file (or possibly incorrectly handing fixed
residues in the PSF/trajectory), it should not do this. I would attempt
to output a two PDB files from the trajectory and look at these with
molecular graphics first.

   trajin mytraj 1 2 1
   trajout mypdb pdb

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Received on Thu Jul 28 2005 - 00:53:01 PDT
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