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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Received on Sun May 18 2008 - 06:07:38 PDT
