Dear experts,
I have been using H++ to prepare any PDB files for simulation. I basically
take the coordinate and topology files from H++ result and then create a
new PDB to run for simulation. I basically copy and paste the .crd and .top
files in new txt files and then run the "ambpdb" command as follows. It
used to work perfectly until few weeks back. But now when I try to run the
same PDB files from H++ I get error message in Amber.
ambpdb -p complex.top < complex.crd > new2.pdb
| ambpdb (C++) Version V15.00
| Reading Amber restart from STDIN
Error: AmberRestart::setupTrajin(): When attempting to read in
Error: box coords/velocity info got 1975 chars, expected 0, 37,
Error: 73, or 144321.
Error: This usually indicates a malformed or corrupted restart file.
I used ParmEd as follows and it runs finewith the same .crd and .top files.
Is there any difference between creating new PDB using "ambpdb" Vs ParmEd?
parmed.py -p complex.top -c complex.crd
ParmEd: a Parameter file Editor
Loaded Amber topology file h27r.top with coordinates from h27r.crd
Reading input from STDIN...
> outpdb new2.pdb
Writing PDB file new2.pdb renumbering atoms and residues
quit
I would really appreciate your help on this.
AP
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Received on Fri Apr 29 2016 - 07:00:04 PDT
