It sounds like the kind of format you could use VMD with. I imagine you
could do all the analysis in VMD also, but in the worst case scenario you
could load it in VMD and then save it as an AMBER trajectory from there.
~Aron
On Sat, Mar 3, 2012 at 11:10 AM, Dmitry Osolodkin <divanych.rambler.ru>wrote:
> Dear AMBER list,
>
> I have a problem with externally generated PDB trajectory which I want
> to analyse with ptraj. Namely, when I take it to ptraj using the first
> frame as topology file, it says:
>
> WARNING in checkCoordinates(): The actual number of atoms (35596304)
> does not match the expected number of atoms (17692) in
> (movie_filtered.pdb)
> With this version of the code, this will likely lead to program
> failure!!!
>
> PTRAJ: rms first out CA.rms .CA
> Mask [.CA] represents 1142 atoms
> [No output trajectory specified (trajout)]
> movie_filtered.pdb: 1 frames.
>
> Obviously, ptraj interprets this trajectory as a single frame. The frame
> delimiters are as follows (each frame consists of 4 chains delimited by
> TER cards):
>
> ATOM 17695 HG3 THR F1713 -1.488 -11.414 -19.211
> TER
> ENDMDL
> MODEL 2
> ATOM 4 HN1 MET B 496 -32.564 32.599 -38.266
>
> How should I modify the pdb trajectory to make it properly readable for
> ptraj?
>
> Thank you in advance.
>
> Dmitry.
>
> --
> Dmitry Osolodkin, PhD
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: dmitry_o.qsar.chem.msu.ru
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sat Mar 03 2012 - 09:00:02 PST
