Re: AMBER: convert_trajectory

From: Wei Chen <gtg553p.mail.gatech.edu>
Date: Wed, 27 Jul 2005 22:06:28 -0400

Hi,

I added [start end offset] following "trajin mytraj" .
Output is correct, although the numbering of residues begins from 2.

Thank you very much!

Wei Chen

"Thomas E. Cheatham, III" <cheatham.chpc.utah.edu>:

>
> > 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 - 03:53:00 PDT
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