Yes. VMD numbering starts at 0. Chimera and cpptraj start at 1.
On Sunday, October 4, 2020, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> Ok, this change has fixed the problem and it is saving PDB files as
> expected.
> I visualized the trajectory in vmd which starts with 0, thus assumed that
> it should be true for AmberTools.
> Great, there is something new to (re)learn every day with Amber.
> Thanks a lot for responding on a Sunday.
>
> On Sun, Oct 4, 2020 at 7:16 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Sun, Oct 4, 2020 at 12:33 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> > wrote:
> > > trajout 4ZF6_solv.pdb pdb multi nobox dumpq onlyframes 0,49,99
> >
> > Cpptraj expects frame #s to start from 1, so I suspect the issue here
> > is that since frame "0" is never encountered, the 'onlyframes' never
> > moves on from it. I thought I had trapped this but I guess not. I'll
> > work on an update to make sure this case is trapped - in the meantime
> > adjust your frame #s so that they start from 1 and see if that fixes
> > things.
> >
> > -Dan
> >
> > >
> > > Cpptraj output on the terminal
> > > [user.localhost MD-4ZF6-3--15]$ cpptraj -i traj-pqr-cpptraj.in
> > >
> > > CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.11)
> > > ___ ___ ___ ___
> > > | \/ | \/ | \/ |
> > > _|_/\_|_/\_|_/\_|_
> > >
> > > | Date/time: 10/04/20 09:59:54
> > > | Available memory: 36.464 GB
> > >
> > > INPUT: Reading input from 'traj-pqr-cpptraj.in'
> > > [parm 4ZF6_solv.prmtop]
> > > Reading '4ZF6_solv.prmtop' as Amber Topology
> > > Radius Set: modified Bondi radii (mbondi)
> > > [trajin 4ZF6_solv-prod300.nc 1 200]
> > > Reading '4ZF6_solv-prod300.nc' as Amber NetCDF
> > > [strip :WAT ]
> > > STRIP: Stripping atoms in mask [:WAT]
> > > [trajout 4ZF6_solv.pdb pdb multi nobox dumpq onlyframes 0,49,99]
> > > Saving frames 0 49 99
> > > Writing '4ZF6_solv.pdb' as PDB
> > > ---------- RUN BEGIN -------------------------------------------------
> > >
> > > PARAMETER FILES (1 total):
> > > 0: 4ZF6_solv.prmtop, 61611 atoms, 18513 res, box: Orthogonal, 18052
> mol,
> > > 18037 solvent
> > >
> > > INPUT TRAJECTORIES (1 total):
> > > 0: '4ZF6_solv-prod300.nc' is a NetCDF AMBER trajectory with
> coordinates,
> > > time, box, Parm 4ZF6_solv.prmtop (Orthogonal box) (reading 200 of 2000)
> > > Coordinate processing will occur on 200 frames.
> > >
> > > OUTPUT TRAJECTORIES (1 total):
> > > '4ZF6_solv.pdb' (200 frames) is a PDB file (1 file per frame),
> writing
> > > charges to occupancy column and GB radii to B-factor column no box
> info,:
> > > Writing frames 0 49 99
> > >
> > > BEGIN TRAJECTORY PROCESSING:
> > > .....................................................
> > > ACTION SETUP FOR PARM '4ZF6_solv.prmtop' (1 actions):
> > > 0: [strip :WAT ]
> > > Stripping 54111 atoms.
> > > Stripped topology: 7500 atoms, 476 res, box: Orthogonal, 15 mol
> > > .....................................................
> > > ACTIVE OUTPUT TRAJECTORIES (1):
> > > 4ZF6_solv.pdb (coordinates, time)
> > > ----- 4ZF6_solv-prod300.nc (1-200, 1) -----
> > > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> > >
> > > Read 200 frames and processed 200 frames.
> > > TIME: Avg. throughput= 490.0916 frames / second.
> > >
> > > ACTION OUTPUT:
> > > TIME: Analyses took 0.0000 seconds.
> > >
> > > RUN TIMING:
> > > TIME: Init : 0.0001 s ( 0.02%)
> > > TIME: Trajectory Process : 0.4081 s ( 99.69%)
> > > 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 : 0.0012 s ( 0.00%)
> > > TIME: Run Total 0.4094 s
> > > ---------- RUN END ---------------------------------------------------
> > > TIME: Total execution time: 0.6527 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.
> > >
> > >
> > >
> > > --
> > >
> > > 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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> >
>
>
> --
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
Elvis
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Received on Sun Oct 04 2020 - 10:00:02 PDT
