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
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Received on Wed Oct 07 2020 - 06:00:04 PDT
