In general cpptraj has more functionality, can be faster (particularly
when processing netcdf trajectories), has better error handling, will
usually give more informative error messages, and is better supported
(ptraj is not longer being actively developed as far as I know).
-Dan
On Mon, Oct 6, 2014 at 1:15 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> I really have not tried to load this script to the cpptraj. In case of
> those trajectory there were some problems with the periodicity so I was
> looked for the possibility to fix it using correct restr file. Are there
> any difference between processing algorithms in cpptraj and ptraj?
>
> James
>
> 2014-10-03 16:09 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> Hi,
>>
>> Does it work in cpptraj?
>>
>> -Dan
>>
>> On Fri, Oct 3, 2014 at 6:13 AM, James Starlight <jmsstarlight.gmail.com>
>> wrote:
>> > Dear Amber users!
>> >
>> > Recently I've faced with the problem of processing of one of my netcdf
>> > trajectory using ptraj:
>> >
>> >
>> > #ptraj protein.parm7 cpptraj.in
>> >
>> > trajin md.nc 4227 last 2
>> > reference protein.inpcrd
>> >
>> > as the result I've obtained:
>> >
>> > ERROR in ptrajProcessInputCoordinates(): Getting cell lengths: NetCDF:
>> > Attempt to convert between text & numbers
>> >
>> > I've load another trajectories with the same sequences of the commands
>> and
>> > no errors have been during its processing. Is it possible to fix it by
>> > conversion to another trajectory format for instance (there is no any
>> > problems with the loading of this trajectory in the VMD)?
>> >
>> > James
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > 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)
>>
>> _______________________________________________
>> 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
--
-------------------------
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 Mon Oct 06 2014 - 08:30:03 PDT
