On Fri, May 8, 2015 at 10:44 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>> cpptraj. What am I missing? My cpptraj says it's V15.00b.
One more note: you're using a beta version of cpptraj - you should get
the official AmberTools15 release. FYI in the AmberTools15 version the
'checkoverlap' command is recognized (but 'around' still isn't yet
implemented - it's on the to-do list).
-Dan
>>>
>>
>> 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
> (801) 585-6208 (Fax)
--
-------------------------
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 Wed May 13 2015 - 15:00:03 PDT
