On Fri, May 8, 2015 at 10:28 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, May 8, 2015 at 12:12 PM, Aronica, Pietro <
> pietro.aronica07.imperial.ac.uk> wrote:
>
>> Hello,
>> Did something happen to the checkoverlap command in cpptraj? Not only I
>> cannot find it in the manual, but when doing "help checkoverlap" within
>> cpptraj itself it gives the help text for the check command. Did the
>> functionality of searching for close contacts between two masks get
>> transferred to a different command? I can issue the command as I need it to
>> be with an older version of ptraj, but cannot find the equivalent in
>> cpptraj. What am I missing? My cpptraj says it's V15.00b.
>>
>
> Look at the "check" and "checkstructure" commands in cpptraj, which
> encapsulates what "checkoverlap" does (and adds more checks, I think). See
> page 559 of the Amber15.pdf manual.
Jason is correct. It is so named because the command does not only
look for atomic overlaps, it will also look for abnormal bond lengths.
The command can also be used to skip frames with abnormalities. Note
that this command is OpenMP parallelized and will be faster when run
with cpptraj.OMP.
-Dan
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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--
-------------------------
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
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Received on Fri May 08 2015 - 10:00:04 PDT
