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
>
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Received on Sun Oct 04 2020 - 07:00:02 PDT
