Can you try excluding '-c tleb_solv.inpcrd' from command line and use
parm ...
trajin tleb_solv.inpcrd
...
in your fixatord.in?
make sure to double check what '-c' is used for (cpptraj --help)
PS: I myself normally use "cpptraj -i my.in", which put everything in that "
my.in" file.
Hai
On Wed, Aug 24, 2016 at 1:15 AM, Andrew Schaub <aschaub.uci.edu> wrote:
> 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 >
> fixatord.out
> Error: Atom 6315 was assigned a lower molecule # than previous atom.
> Error: This can happen if bond information is incorrect or missing, or if
> the
> 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
> fixed
> [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]
> ---------- RUN BEGIN -------------------------------------------------
> Warning: No input trajectories specified.
>
> RUN TIMING:
> 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 ---------------------------------------------------
> [quit]
> 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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>
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Received on Tue Aug 23 2016 - 23:00:02 PDT
