Dear All,
I managed to fix it.
It was related to the wrong bonding that I had chosen in tleap script.
After fixing the pdb, the freshly generated prmtop/inpcrd files are ok as
checked by parmed with checkvalidity command.
thanks
On Mon, May 3, 2021 at 1:46 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> 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,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> 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
>
> P Please consider the environment before printing this e-mail
>
>
--
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,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
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
P Please consider the environment before printing this e-mail
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Received on Mon May 03 2021 - 05:30:04 PDT
