Hi,
Have you tried cpptraj? It should be able to handle PDB files with
multiple models correctly.
-Dan
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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Received on Sat Mar 03 2012 - 11:00:04 PST
