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
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Received on Thu Sep 10 2020 - 06:30:02 PDT
