Hi,
Glad you managed to fix it. FYI more recent versions of cpptraj (from
e.g. GitHub or AmberTools 21) can actually handle molecules with
non-sequential atom ordering. Also, the more recent versions will
properly parse CMAP terms. So I recommend using a more recent version
of cpptraj.
-Dan
On Mon, May 3, 2021 at 8:18 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> 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 - 06:00:09 PDT
