AMBER Archive (2008)

Subject: AMBER: reading PDB trajectory

From: Mark Abraham (Mark.Abraham_at_anu.edu.au)
Date: Thu May 15 2008 - 22:49:55 CDT

Hi,

I'm attempting to convert a trajectory from a GROMACS format to Amber's
mdcrd format so that I can run some energy re-evaluations using sander.
When testing I made a 532-atom 2-frame PDB-format pseudo-trajectory with
well-placed TER and MODEL/ENDMDL pairs. Then I tried to read that with
Amber 9's ptraj, but it read it as a single 1064-atom frame and gave a
message complaining that it didn't match my 532-atom prmtop...

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin 1oeh_00001_cluster_0.pdb
   Checking coordinates: 1oeh_00001_cluster_0.pdb
   WARNING in checkCoordinates(): The actual number of atoms (1064)
   does not match the expected number of atoms (532) in
(1oeh_00001_cluster_0.pdb)
   With this version of the code, this will likely lead to program
failure!!!

A segfault followed when trying to output in mdrcd format.

Is there a better way to do this operation than to write a large number
of single-structure PDB files and get ptraj to read them in singly? If
so, what?

I can see in getCoordinatesFromPdb() in src/ptraj/trajectory.c that the
PDB reader scans only for ATOM/HETATM records and assumes there's only
one structure. To me, this hack seems closer to a bug than a feature :-)

Mark
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