Hello. I am experiencing some issues with ambertools 13 while trying to
analyse different systems. The first system is a "normal" pmemd.cuda
simulation of a protein in water. When I type the command cpptraj -i
rmsd.ptraj -p HOH_wat.prmtop, I get the following error:
CPPTRAJ: Trajectory Analysis. V13.1
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file rmsd.ptraj
[trajin mdcrd.md2]
Warning: Could not get parameter file:
Warning: parmname=, pindex=0
Error: TrajectoryFile: Parm file is null.
Error: trajin: Could not set up trajectory.
But when I type cpptraj -p HOH_wat.prmtop -i rmsd.ptraj, I get
CPPTRAJ: Trajectory Analysis. V13.1
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| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: [default_name]
Radius Set: ArgH and AspGluO modified Bondi2 radii (mbondi3)
Error: Atom 5311 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing.
Error: Detected # of molecules is 7615. If this is incorrect and your
Error: topology does not have bond information (e.g. PDB file), try
Error: increasing the bond search cutoff offset (currently 0.200000).
Error: e.g. 'parm HOH_wat.prmtop bondsearch <new offset>'
Error: This can also happen if the atoms in your molecules are not
Error: sequential (e.g. molecule 1 is atoms 1-4,10-14 and molecule 2
Error: is atoms 5-9,15-20). This can be fixed using the 'setMolecules'
Error: command in parmed.py.
Error: Could not open parm HOH_wat.prmtop
The other system is a protein in a lipid membrane, and I only get the error
when I type, cpptraj -i rmsd.ptraj -p prmtop, i.e., when the input file
comes before the topology.
I am running Ubuntu 12.04 and I have compiled amber and ambertools using
the default settings. ./configure gnu and make install (after that a
parallel compilation). I could not compile the openmp version, but I will
send an email afterwards on that topic.
I didn't have any of this issues with ambertools 12. Please, let me know if
you want a copy of any of the files from the simulation.
Thank you
Fabrício Bracht
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Received on Wed Jun 19 2013 - 10:00:03 PDT
