[AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj

From: Andrew Schaub <aschaub.uci.edu>
Date: Wed, 24 Aug 2016 14:15:58 +0900

Good Afternoon,

I am trying to perform a simulation on a P450 enzyme with a heme. This
appears to be very similar to the tutorial (
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm), so I
have been following this to setup my system in Amber16. I have managed to
generate .prmtop and .inpcrd files from MCPB and g09 outputs, and am able
to minimize the system, but am unable to verify the modeling.

$ source /opt/amber16-mpi/amber.sh

$ cpptraj -p tleb_solv.prmtop -c tleb_solv.inpcrd -i fixatord.in >
Error: Atom 6315 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing, or if
Error: atom numbering in molecules is not sequential. Try one of the
Error: following:
Error: - If this is a PDB file, try using the 'noconect' keyword.
Error: - If this topology did not have bond info, try increasing the bond
Error: search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
Error: - Use the 'fixatomorder' command to reorder the topology and any
Error: associated coordinates.
Error: - Use the 'setMolecules' command in parmed to reorder only the
Error: topology.
Error: Could not determine molecule information for tleb_solv.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for tleb_solv.prmtop.

$ cat fixatord.out

CPPTRAJ: Trajectory Analysis. V16.12
    ___ ___ ___ ___
     | \/ | \/ | \/ |

| Date/time: 08/24/16 14:08:34
| Available memory: 45.010 GB

    Reading 'tleb_solv.prmtop' as Amber Topology
    Reading 'tleb_solv.inpcrd' as Amber Restart
    Setting active reference for distance-based masks: 'tleb_solv.inpcrd'
INPUT: Reading input from 'fixatord.in'
  [fixatomorder outprefix fixed]
Warning: Action specified before trajin/ensemble. Assuming trajin.
    FIXATOMORDER: Will attempt to fix atom ordering when atom numbering in
molecules is non-sequential. Re-ordered topology will be output with prefix
  [trajout fixed.tleb_solv.inpcrd]
Warning: Format not specified and extension '.inpcrd' not recognized.
Defaulting to Amber Trajectory.
    Writing 'fixed.tleb_solv.inpcrd' as Amber Trajectory
---------- RUN BEGIN -------------------------------------------------
Warning: No input trajectories specified.

TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 0.0000 s ( 0.00%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 16.67%)
TIME: Other : 0.0000 s ( 0.83%)
TIME: Run Total 0.0000 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.1311 seconds.
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., 2013, 9 (7), pp 3084-3095.

I'm unable to fix the atom order, as it can't seem to find an input
trajectory. I am able though to minimize the original prmtop/inpcrd system,
though I am unable to view the .rst files in VMD or Chimera. I am able to
view the inpcrd file in VMD or Chimera.

Best Regards,

Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Tue Aug 23 2016 - 22:30:03 PDT
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