Hi,
It seems like your DCD file may be corrupted. The block in question (size
48) pertains to the box coordinates. Does cpptraj print out any other
warnings when you load the trajectory or during processing?
If your trajectory is corrupted I'm not sure if there is any way to recover
it, since all the bytes following the corruption may now be out of
alignment. You could try setting the debug level higher before loading to
get some extra info, e.g.:
debug trajin 5
trajin mytraj.dcd
but you may need to just write those frames off as lost.
-Dan
On Sat, Feb 21, 2015 at 2:21 PM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> I am sorry, VMD does not read all the frames, it reads up to 3660.
> According to catdcd the total number of frames is 5500. The log file also
> says that 5500 frames were written to the dcd file (the simulation was
> conducted with NAMD using amber topologies).
>
>
>
> On 21 February 2015 at 23:06, Thomas Evangelidis <tevang3.gmail.com>
> wrote:
>
> > Is there any way to fix this error? I am trying to strip atoms from a dcd
> > file with cpptraj but I get this error and only a portion of the frames
> > is written. Remarkably, VMD can read all the frames of the dcd file.
> > catdcd & trjconv also stop at the same point as cpptraj.
> >
> >
> >
> > --
> >
> > ======================================================================
> >
> > Thomas Evangelidis
> >
> > PhD student
> > University of Athens
> > Faculty of Pharmacy
> > Department of Pharmaceutical Chemistry
> > Panepistimioupoli-Zografou
> > 157 71 Athens
> > GREECE
> >
> > email: tevang.pharm.uoa.gr
> >
> > tevang3.gmail.com
> >
> >
> > website: https://sites.google.com/site/thomasevangelidishomepage/
> >
> > ===============================================================
> >
> > *Physics is the only real science. The rest are just stamp collecting.*
> >
> > *- Ernest Rutherford*
> >
> >
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
> ===============================================================
>
> *Physics is the only real science. The rest are just stamp collecting.*
>
> *- Ernest Rutherford*
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Feb 21 2015 - 14:00:02 PST
