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 - 08:30:02 PST
