Dear All,
Amber top/crd files created for MD with a 614 residue protein gave no error
in tleap and the structure looks fine after minimization/heat/equil steps.
But while trying to save pdb or converting trajectory from nc to crd format
with cpptraj I'm getting the following errors and crd file is not being
saved.
I tried the fixatomorder as suggested by the error message but in vain.
Below are my cpptraj input and error message.
Can you please help me understand if my prmtop/inpcrd files have
something wrong and if so why the MD is still running like usual?
What else can I try to fix the prmtop and is it better to run MD with fixed
topology files?
Looking forward to valuable suggestions from developers and list.
thank you and best regards.
cpptraj input
parm 1bvy-af-solv.prmtop
trajin final.1.nc
fixatomorder
parmwrite out 1bvy-af-solv-fix.prmtop
parm 1bvy-af-solv-fix.prmtop [top1]
trajin final.1.nc top1
autoimage
trajout final.1.crd
quit
cpptraj output
CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.09)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 05/03/21 17:13:09
| Available memory: 25.971 GB
INPUT: Reading input from 'equil-cpptraj.in'
[parm 1bvy-af-solv.prmtop]
Reading '1bvy-af-solv.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
Warning: Amber topology flag 'CMAP_COUNT' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_RESOLUTION' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_01' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_02' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_03' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_04' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_05' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_06' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_07' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_08' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_09' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_10' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_11' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_12' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_13' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_14' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_INDEX' is unrecognized and will be
skipped.
Error: Atom 9656 was assigned a lower molecule # (1) than previous atom (2).
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 1bvy-af-solv.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for 1bvy-af-solv.prmtop.
[trajin final.1.nc]
Reading 'final.1.nc' as Amber NetCDF
[fixatomorder]
FIXATOMORDER: Will attempt to fix atom ordering when atom numbering
in molecules is non-sequential.
[parmwrite out 1bvy-af-solv-fix.prmtop]
Writing topology 0 (1bvy-af-solv.prmtop) to
'1bvy-af-solv-fix.prmtop' with format Amber Topology
[parm 1bvy-af-solv-fix.prmtop [top1]]
Reading '1bvy-af-solv-fix.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
Error: Atom 9656 was assigned a lower molecule # (1) than previous atom (2).
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 1bvy-af-solv-fix.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for 1bvy-af-solv-fix.prmtop.
[trajin final.1.nc top1]
Reading 'final.1.nc' as Amber NetCDF
Error: [trajin] Not all arguments handled: [ top1 ]
1 errors encountered reading input.
TIME: Total execution time: 0.5720 seconds.
Error: Error(s) occurred during execution.
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Mon May 03 2021 - 01:30:02 PDT
