On Mon, Jan 20, 2020 at 5:26 AM emanuele falbo <falbo.emanuele.gmail.com> wrote:
>
> So, I am assuming that those warnings are due to the fact that the new
> cpptraj version
> is essentially meant to read just netcfd, and thus I can clearly ignore
> them ? Am I right ?
No - you almost certainly have some sort of corruption. Since 'check'
returned nothing, it is likely the issue is a truncated last frame
(scenario 2 in my initial reply). Is 'fixed.corrupted.mdcrd' smaller
than 'corrupted.mdcrd'?
-Dan
>
> Regards,
> Manuele
>
> Il giorno ven 17 gen 2020 alle ore 18:48 Daniel Roe <daniel.r.roe.gmail.com>
> ha scritto:
>
> > Hi,
> >
> > This error could be innocuous, or it could be a problem. The issue is
> > that the ASCII trajectory format doesn't store how many atoms or
> > frames it has, so cpptraj tries to guess based on the expected
> > trajectory size (calculated from the number of atoms in the topology,
> > the size of the title, whether REMD lines are present etc). There can
> > be a few reasons why this fails:
> >
> > 1) Most common: you are providing a topology with a different number
> > of atoms than was used to generate the trajectory. Double check that
> > the topology used in the simulation that generated the trajectory is
> > the one you are using. This can also happen if you e.g. load a
> > stripped trajectory with the original topology etc.
> > 2) Somewhat common: your simulation crashed and the trajectory
> > contains an incomplete frame. In this case cpptraj will read all of
> > the "good" frames. If the corrupted frame is in the middle of the
> > trajectory somehow this is bad and will fail. You should run the
> > 'check' command on this trajectory to make sure things look ok.
> > 3) Uncommon: Somehow you got some extra bytes in the file, maybe an
> > extra newline at the end? This can happen if e.g. you opened up the
> > trajectory in a text editor and accidentally hit "enter" or something.
> >
> > Note that all of these become a non-issue if you use the default
> > netcdf trajectory format.
> >
> > -Dan
> >
> > On Fri, Jan 17, 2020 at 11:04 AM emanuele falbo
> > <falbo.emanuele.gmail.com> wrote:
> > >
> > > Dear users,
> > >
> > > I have used packmol to make a leap input file (the input packmol file is
> > a
> > > pdb),
> > > and the dynamics seems going perfectly. When getting the RDF from the
> > > trajectory using cpptraj I get the following error from cpptraj:
> > >
> > >
> > >
> > > *"Warning: 04_Prod_2.mdcrd: Could not accurately predict # frames. This
> > > usuallyWarning: indicates a corrupted trajectory or
> > > trajectory/topologyWarning: mismatch. Will attempt to read 277 frames.*
> > >
> > > However, cpptraj terminates the RDF calculation without problems.
> > > I do not know whether this error could be ignored, and thus
> > > the RDF can be trustable, or not. Do you have any suggestion ?
> > >
> > > Cheers,
> > > Manuele
> > >
> > > --
> > >
> > > *Emanuele Falbo*
> > > PhD student
> > > Penfold group
> > > School of Natural and Environmental Sciences
> > > Bedson Building, Newcastle University
> > > Newcastle upon Tyne, NE1 7RU
> > > w: http://tompenfoldresearch.weebly.com/
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>
> --
>
> *Emanuele Falbo*
> PhD student
> Penfold group
> School of Natural and Environmental Sciences
> Bedson Building, Newcastle University
> Newcastle upon Tyne, NE1 7RU
> w: http://tompenfoldresearch.weebly.com/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jan 21 2020 - 11:30:02 PST
