Hi
Sorry my bad I ignored the onlyframes flag
Can you try this one
trajout 4ZF6_solv.prmtop.pqr pdb multi nobox dumpq noter 1 last 10
Best Regards
Elvis
On Wed, 7 Oct 2020 at 18:05, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> Dear Elvis and other Amber people,
> Strangely your suggestion isn't working at my end.
> With the following command options I'm getting only one PDB file i.e. the
> first one.
>
> trajout 4ZF6_solv.pqr pdb multi nobox dumpq onlyframes 1 last 50
>
> Following is the cpptraj output on the terminal shows (in bold) that it is
> writing only 1 frame.
> Can you please suggest what might be going wrong here and how to fix it?
>
> (base) [exx.c107739 4ZF6-3--15]$ cpptraj -i MD-4ZF6-3--15/cpptraj.in
>
> CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.09)
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 10/07/20 16:57:55
> | Available memory: 5.063 GB
>
> INPUT: Reading input from 'MD-4ZF6-3--15/cpptraj.in'
> [parm MD-4ZF6-3--15/4ZF6_solv.prmtop]
> Reading 'MD-4ZF6-3--15/4ZF6_solv.prmtop' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> [trajin MD-4ZF6-3--15/4ZF6_solv-prod300.nc 1 2000]
> Reading 'MD-4ZF6-3--15/4ZF6_solv-prod300.nc' as Amber NetCDF
> [strip :WAT ]
> STRIP: Stripping atoms in mask [:WAT]
> [trajout 4ZF6_solv.prmtop.pqr pdb multi nobox dumpq noter onlyframes 1
> last 10]
> * Saving frames 1*
> Writing '4ZF6_solv.prmtop.pqr' 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 2000 of 2000)
> Coordinate processing will occur on 2000 frames.
>
> OUTPUT TRAJECTORIES (1 total):
> '4ZF6_solv.prmtop.pqr' (2000 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 1*
>
> 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.prmtop.pqr (coordinates, time)
> ----- 4ZF6_solv-prod300.nc (1-2000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 2000 frames and processed 2000 frames.
> TIME: Avg. throughput= 268.0487 frames / second.
>
> ACTION OUTPUT:
> TIME: Analyses took 0.0000 seconds.
>
> RUN TIMING:
> TIME: Init : 0.0001 s ( 0.00%)
> TIME: Trajectory Process : 7.4613 s ( 99.98%)
> 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 : 0.0011 s ( 0.00%)
> TIME: Run Total 7.4626 s
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 7.7751 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.
>
>
> On Tue, Oct 6, 2020 at 9:46 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > Dear Elvis,
> > OK, that seems intuitive and obvious now.
> > thanks for the quick response.
> > best regards
> >
> > On Tue, Oct 6, 2020 at 9:36 AM Elvis Martis <elvis_bcp.elvismartis.in>
> > wrote:
> >
> >> Hi
> >> you could try this
> >> trajout output.pdb pdb multi nobox dumpq noter onlyframes 1 last 10,
> >> (first
> >> is a start frame, followed by the last frame, and the offset; save every
> >> 10th frame in this case)
> >>
> >> Best Regards
> >> Elvis
> >>
> >>
> >>
> >> On Tue, 6 Oct 2020 at 09:29, Vaibhav Dixit <vaibhavadixit.gmail.com>
> >> wrote:
> >>
> >> > Dear Daniel and All,
> >> > Is it possible to write snapshots at regular intervals with a
> specified
> >> > increment like the following without actually writing all the numbers
> in
> >> > the cpptraj input?
> >> > Snapshot number 1,10,20,30,40.... or
> >> > 1,50,100,150,200,250...
> >> >
> >> > I can run a for loop to write numbers for all snapshots but I'm
> guessing
> >> > cpptraj must have equivalent options that I can't figure out myself
> and
> >> > thus possible to easily avoid having to do this
> >> > list=()
> >> > for i in {1..20000..50}; do list+=$i; list+=", " : done)
> >> > trajout output.pdb pdb multi nobox dumpq noter onlyframes $list
> >> >
> >> > I will use the pqr format to be used later for electrostatics
> >> > calculations.
> >> > Looking forward to some valuable suggestions.
> >> > Thank you and best regards.
> >> >
> >> > On Sun, Oct 4, 2020 at 10:01 PM Elvis Martis <
> elvis_bcp.elvismartis.in>
> >> > wrote:
> >> >
> >> > > Yes. VMD numbering starts at 0. Chimera and cpptraj start at 1.
> >> > >
> >> > > On Sunday, October 4, 2020, Vaibhav Dixit <vaibhavadixit.gmail.com>
> >> > wrote:
> >> > >
> >> > > > Ok, this change has fixed the problem and it is saving PDB files
> as
> >> > > > expected.
> >> > > > I visualized the trajectory in vmd which starts with 0, thus
> assumed
> >> > that
> >> > > > it should be true for AmberTools.
> >> > > > Great, there is something new to (re)learn every day with Amber.
> >> > > > Thanks a lot for responding on a Sunday.
> >> > > >
> >> > > > On Sun, Oct 4, 2020 at 7:16 PM Daniel Roe <daniel.r.roe.gmail.com
> >
> >> > > wrote:
> >> > > >
> >> > > > > Hi,
> >> > > > >
> >> > > > > On Sun, Oct 4, 2020 at 12:33 AM Vaibhav Dixit <
> >> > vaibhavadixit.gmail.com
> >> > > >
> >> > > > > wrote:
> >> > > > > > trajout 4ZF6_solv.pdb pdb multi nobox dumpq onlyframes 0,49,99
> >> > > > >
> >> > > > > Cpptraj expects frame #s to start from 1, so I suspect the issue
> >> here
> >> > > > > is that since frame "0" is never encountered, the 'onlyframes'
> >> never
> >> > > > > moves on from it. I thought I had trapped this but I guess not.
> >> I'll
> >> > > > > work on an update to make sure this case is trapped - in the
> >> meantime
> >> > > > > adjust your frame #s so that they start from 1 and see if that
> >> fixes
> >> > > > > things.
> >> > > > >
> >> > > > > -Dan
> >> > > > >
> >> > > > > >
> >> > > > > > Cpptraj output on the terminal
> >> > > > > > [user.localhost MD-4ZF6-3--15]$ 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
> >> > > > > > _______________________________________________
> >> > > > > > AMBER mailing list
> >> > > > > > AMBER.ambermd.org
> >> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > > >
> >> > > > > _______________________________________________
> >> > > > > AMBER mailing list
> >> > > > > AMBER.ambermd.org
> >> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > > >
> >> > > >
> >> > > >
> >> > > > --
> >> > > >
> >> > > > 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
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> >
> >> >
> >> > --
> >> >
> >> > 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
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> >
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
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Received on Wed Oct 07 2020 - 06:00:05 PDT
