Hi,
You can use the '-xa' command line flag to add output trajectory arguments, e.g.
cpptraj -p tz2.truncoct.parm7 -y tz2.truncoct.nc -x temp.nc -xa nobox
See the manual and 'cpptraj --help' for full details on command line arguments.
-Dan
On Mon, Aug 8, 2022 at 4:50 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
>
> One more question:
> is it possible to remove PBC from the input trajectory during the
> conversion using
> cpptraj -p protein.pdb -y my_trajectory.netcdf -x test.xtc
> ?
>
> Il giorno lun 25 lug 2022 alle ore 10:48 Enrico Martinez
> <jmsstarlight.gmail.com> ha scritto:
> >
> > Right, thank you very much!
> > Cheers
> > Enrico
> >
> > пт, 22 июл. 2022 г. в 16:20, Daniel Roe <daniel.r.roe.gmail.com>:
> > >
> > > Hi,
> > >
> > > On Fri, Jul 15, 2022 at 10:16 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
> > > >
> > > > Great, thank you very much Daniel!
> > > > Is it possible to use cpptraj in this manner for the trajectory
> > > > analysis (similar to the gromacs syntax without any additional batch
> > > > files specifying options): when one command in Linux terminal with all
> > > > options is related to the particular analysis? If yes, when could I
> > >
> > > In general no. While cpptraj has some command-line utility (trajectory
> > > conversion, atom mask selection, etc), the primary ways to use it for
> > > analysis are via input scripts and interactively.
> > >
> > > -Dan
> > >
> > > > see the tutorial ?
> > > > Cheers
> > > > Enrico
> > > >
> > > > пт, 15 июл. 2022 г. в 13:58, Daniel Roe <daniel.r.roe.gmail.com>:
> > > > >
> > > > > You're in luck! Cpptraj will do this conversion for you, e.g.:
> > > > >
> > > > > cpptraj -p protein.pdb -y my_trajectory.netcdf -x test.xtc
> > > > >
> > > > > Make sure you're using an up-to-date version of cpptraj (GitHub or
> > > > > AmberTools 22).
> > > > >
> > > > > -Dan
> > > > >
> > > > > On Fri, Jul 15, 2022 at 7:42 AM Enrico Martinez via AMBER
> > > > > <amber.ambermd.org> wrote:
> > > > > >
> > > > > > Dear Amber users!
> > > > > > I am looking for a possibility to convert netcdf trajectory produced
> > > > > > by amber to other formats, particularly to xtc accepted by gromacs.
> > > > > > I've tried to use gmx utilite (that worked fine before!):
> > > > > > gmx trjconv -f ${sim}/prod_*.netcdf -s protein.pdb -o test.xtc
> > > > > > -timestep 10 -pbc no
> > > > > >
> > > > > > but it does not work anymore :-)
> > > > > >
> > > > > > -------------------------------------------------------
> > > > > > Program: gmx trjconv, version 2020.1-Ubuntu-2020.1-1
> > > > > >
> > > > > > Standard library logic error (bug):
> > > > > > (exception type: St11logic_error)
> > > > > > basic_string::_M_construct null not valid
> > > > > >
> > > > > > I have tried to use directly vmd and could open the same file without
> > > > > > problem using
> > > > > > vmd -netcdf my_trajectory.netcdf
> > > > > >
> > > > > > is there any way to run vmd in batch without GUI for such conversion?
> > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Aug 08 2022 - 06:00:03 PDT
