This is happening because the coordinates are overflowing, either
because the system is massive or part of it has moved far away from
the coordinate origin. Not knowing the specifics of your system I
can't be sure, but it appears that this problem is with the last atom
in your system, which appears to be very far away from everything else
for some reason. If you are using Amber12 you can use the new netcdf
restart file format (ntxo = 2, see
http://ambermd.org/doc12/ for a
little more info) which can hold larger numbers than the ASCII restart
format. Note that netcdf restarts are currently only supported by
Amber12 sander, pmemd, cpptraj, and NAB.
-Dan
On Wed, Jun 20, 2012 at 3:34 PM, Ashutosh Shandilya
<izerokelvin.gmail.com> wrote:
> Dear Amber users
>
> The coordinate file after simulation (implicit) is showing star mark
> highlighted in the first column. I reran the simulation but again it shows
> the same error and one more observation was that the (x,y,z) coordinate
> values are quite high from the original one. To generate a pdb file if I
> manually give some arbitrary similar value instead of stars and again
> restart the simulation its giving nan values.
>
> 1184.6077849 87.8888422 467.84796201185.3934567 87.3155358 466.8924446
> 1185.2680706 88.7090605 464.54429731186.4476164 89.0831923 464.6623140
> 1184.8475718 87.6484031 463.75189751183.8646739 87.4420910 463.7650775
> 1185.7071448 86.8318350 462.86466941185.0671587 86.3891983 462.1111381
> 1186.3153669 87.5821378 462.35431881186.6158655 85.8276403 463.4688349
> 1187.5664425 85.4647477 462.72178371186.3922755 85.4288019 464.6323917
> ************* *-48.0818384-390.5949655
> 0.0068848 0.0591804 -0.1366963 1.8340742 -0.6580615 -0.6321001
> -0.6970049 0.0615980 -0.9000795 1.2015969 0.2187631 -0.5411940
> 0.1566680 0.3761406 -0.5256694 -0.7715472 -1.1329467 -0.3315136
> 0.8764598 0.0811084 1.0273480 0.2398398 -0.1928732 -0.0443124
> -0.0285152 0.3707692 -0.1225974 -0.0579449 -0.2956305 -0.2325728
> 0.4026198 0.3070977 0.2775148 -0.3166358 -0.2877791 0.1805477
>
> If some one came across this problem and have any clue that would help.
> Thanks
> Ashutosh
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 21 2012 - 05:00:03 PDT
