Hi,
Ok,thanks. The 'fixed.corrupted.mdcrd' (lines=25905001) is indeed smaller
than corrupted.mdcrd (lines=25946416).
Do you know if there's another way to check whether this is valid or not ?
otherwise I'll need to rerun it but with ioutfm=1
Cheers,
Manuele
Il giorno mar 21 gen 2020 alle ore 19:01 Daniel Roe <daniel.r.roe.gmail.com>
ha scritto:
> 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/
> > _______________________________________________
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>
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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/
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Received on Wed Jan 22 2020 - 02:00:02 PST
