What I suspect is happening is that cpptraj is not reading the mass
information from your PSF file correctly (see bugfix 26). Try
recompiling with all current bugfixes (currently up to 33) and see if
that fixes the problem.
-Dan
On Thu, Jan 24, 2013 at 1:47 AM, Vlastimil Zíma <zima.karlov.mff.cuni.cz> wrote:
> Hi,
>
> this week I encountered troubles with cpptraj. I tried to get distance of
> two atoms from DCD trajectory, but cpptraj returned only 0.0 for all frames.
>
> parm ../initial_neutral.psf
> trajin trajectory.dcd
> distance s1_bond1 :1243.O4 :451.HZ1 out poster/k868_popc.dat
>
> When I use geometric center
>
> distance s1_bond1 :1243.O4 :451.HZ1 out poster/k868_popc.dat geom
>
> everything works fine.
>
> I expect some bug in cpptraj. I use Amber Tools 12 with bugfixes 1-24.
>
> VZ
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Jan 24 2013 - 08:00:02 PST
