Glad it was resolved. If you encounter further issues let me know or open
an Issue on the cpptraj GitHub site.
-Dan
On Thu, Sep 10, 2020 at 9:26 AM Marko Sever <
Marko.Sever.ki.si> wrote:
> Weird now I reinstalled Ambertools 20 and it works, don't know what I did
> wrong the first time. Disregard my previous email.
>
>
>
> The debug stuff is useful I will use it if I encounter another problem.
>
>
>
>
>
> Marko
>
>
>
> ________________________________
>
> Od: Daniel Roe <daniel.r.roe.gmail.com>
>
> Poslano: četrtek, 10. september 2020 15:13:48
>
> Za: AMBER Mailing List
>
> Zadeva: Re: [AMBER] problem with cpptraj
>
>
>
> Hi,
>
>
>
> What are the internal version #s of cpptraj where you have the issue
>
> (use cpptraj --internal-version)?
>
>
>
> Can you add 'debug trajin 10' before your 'trajin' command? This will
>
> print out some extra info. Post that info here. E.g.
>
>
>
> parm something.psf
>
> debug trajin 10
>
> trajin mydcd.dcd
>
> quit
>
>
>
> If it's possible to provide me off-list with the PSF/trajectory file
>
> that would also help.
>
>
>
> -Dan
>
>
>
> On Thu, Sep 10, 2020 at 8:57 AM Marko Sever <Marko.Sever.ki.si> wrote:
>
> >
>
> > Hello,
>
> >
>
> >
>
> > I have a problem with cpptraj. I installed it locally on my computer via
> the conda AmberTools installation method, which is provided on the Amber
> website.
>
> >
>
> > The cpptraj program seems to start fine, but when I try to load a
> trajectory after loading the parameters file (psf or pdb) it says that
> there is an error in the number of atoms in the parameter file and in the
> trajectory.
>
> >
>
> >
>
> > Error: # atoms in DCD file (93892) does not match # atoms in parm
> step5_assembly.psf (93854)
>
> > Error: Could not set up 'blabla.dcd' for reading.
>
> > Error: Could not set up input trajectory 'blabla.dcd'.
>
> >
>
> >
>
> > The same parameter file+trajectory works fine on a HPC install od
> amber-18-gcc, in addition it works fine with Charmm, Namd and VMD. So in
> reality there isn't a mismatch between the two.
>
> >
>
> >
>
> > On the HPC I like to use cpptraj very much, it is very fast and would
> like to use it also on my local computer.
>
> >
>
> >
>
> > So there must be something wrong with the install/configuration of
> cpptraj on my local computer.
>
> >
>
> > I tried both the Ambertools version 20 and 19, same behaviour.
>
> >
>
> >
>
> > Can you help me?
>
> >
>
> >
>
> > Regards,
>
> >
>
> > Marko
>
> > _______________________________________________
>
> > 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
>
> _______________________________________________
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Sep 10 2020 - 09:30:02 PDT
