Hi Dan,
Thanks for helping out. So, I realized that AMBER14 outputs ASCII files by
default-that's the version I am using.
However, after having used the check command:
trajin corrupted.mdcrd
check :1-168 skipbadframes silent
trajout fixed.corrupted.mdcrd
I do not get any error from cpptraj. Also, I loaded the fixed trajectory
(fixed.corrupted.mdcrd ) in cpptraj,
and computed the RDFs, and it turns out that the RDFs from the corrected
trajectory
look the same as the ones from the ASCII trajectory (they perfectly
overlap).
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 ?
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/
> > _______________________________________________
> > 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
>
--
*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 Mon Jan 20 2020 - 02:30:01 PST
