Thank you Hai for the quick response. I did as you suggested and that fixed
my issue.
fixatord.in:
fixatomorder outprefix fixed
trajin tleb_solv.inpcrd
trajout fixed.tleb_solv.inpcrd
run
quit
$ cpptraj -p tleb_solv.prmtop -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 14:52:11
| Available memory: 46.000 GB
Reading 'tleb_solv.prmtop' as Amber Topology
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
[trajin tleb_solv.inpcrd]
Reading 'tleb_solv.inpcrd' as Amber Restart
[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 -------------------------------------------------
PARAMETER FILES (1 total):
0: tleb_solv.prmtop, 46568 atoms, 13827 res, box: Orthogonal, 0 mol
INPUT TRAJECTORIES (1 total):
0: 'tleb_solv.inpcrd' is an AMBER restart file, no velocities, Parm
tleb_solv.prmtop (Orthogonal box) (reading 1 of 1)
Coordinate processing will occur on 1 frames.
OUTPUT TRAJECTORIES (1 total):
'fixed.tleb_solv.inpcrd' (1 frames) is an AMBER trajectory
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'tleb_solv.prmtop' (1 actions):
0: [fixatomorder outprefix fixed]
Detected 13433 molecules.
Re-ordered parm: 46568 atoms, 13827 res, box: Orthogonal, 13433 mol,
13410 solvent
Writing topology 0 (tleb_solv.prmtop) to 'fixed.tleb_solv.prmtop' with
format Amber Topology
----- tleb_solv.inpcrd (1-1, 1) -----
100% Complete.
Read 1 frames and processed 1 frames.
TIME: Avg. throughput= 3.8624 frames / second.
ACTION OUTPUT:
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 0.2589 s ( 99.29%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0018 s ( 0.01%)
TIME: Run Total 0.2608 s
---------- RUN END ---------------------------------------------------
[quit]
TIME: Total execution time: 0.4037 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.
$ ls *.inpcrd
$ ls fixed*
fixed.log fixed.tleb_solv.inpcrd fixed.tleb_solv.prmtop
I'll review the cpptraj tutorials and the amber manual per your suggestion.
Thanks again!
Best Regards,
Andrew Schaub
On Wed, Aug 24, 2016 at 2:44 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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/>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 23:00:03 PDT
