Re: [AMBER] Conversion NETCDF trajectory to other formats

From: Daniel Roe via AMBER <amber.ambermd.org>
Date: Mon, 8 Aug 2022 10:10:09 -0400

Hi,

Sorry, I didn't understand your original question. The 'nobox' keyword
will remove the box information, which is what I thought you meant. I
think you meant you wanted to re-image the trajectory. To do any
actions in cpptraj you need to use an input script or a here document.
Accepting actions from the command line would have to be added as a
feature. You can add a feature request to the GitHub site if you want:
https://github.com/Amber-MD/cpptraj/issues

Hope this helps,

-Dan

On Mon, Aug 8, 2022 at 9:53 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
>
> Thank you!
> Just a few additional questions:
> -xa nobox is like autoimage provided in the batch script ?
> Or do I need both of them ??
>
> Do we need to remove PBC for the post-processing analysis like MMPBSA.py ?
>
> Il giorno lun 8 ago 2022 alle ore 14:35 Daniel Roe via AMBER
> <amber.ambermd.org> ha scritto:
> >
> > 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?
> > > > > > > >
> > > > > > > > _______________________________________________
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> > > > > > > > AMBER.ambermd.org
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> >
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Received on Mon Aug 08 2022 - 07:30:03 PDT
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