It means that those two atoms ended up with positions more than
9999.9 A away from the
center of the xplor coordinate system.
It can happen with very big systems, or with systems that aren't
covalently bonded.
Did you forget to include some intermolecular NOEs?
But it's most common to see it in cases where some potential term
wasn't set up correctly.
If a particular term is generating very high energy & force, it can
end up throwing an atom
out into space.
Take a look at the energies reported by xplor during your dynamics
trajectory. Is one term
very large? Is the IVM taking extremely short timesteps? That might
put you on the right track.
--JK
On Jun 15, 2007, at 5:21 AM, Marco Roeben wrote:
> Hello everyone,
>
> could someone explain the following error message to me? I've no
> clue what has
> happened. Thank you very much!
>
>
> PublicIVM::syncPos: recentering atoms
> cm: { -174.615, 6925.09, -5895.56 }
> %ATMCHK-ERR: unknown coordinates for atom " -6 -PHE -CD2 "
> %ATMCHK-ERR: unknown coordinates for atom " -6 -PHE -HD2 "
> %ATMCHK-ERR: Unknown coordinates
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> BOMLEV= 0 reached. Program execution will be terminated.
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Subroutine DIE called . Terminating
>
>
> with best regards
> Marco
>
> --
> Dipl. Chem. Marco R?ben
> Leibniz-Institut f?r Molekulare Pharmakologie Berlin (FMP)
> Abt.: NMR-unterst?tzte Strukturforschung
> Robert-R?ssle-Str. 10
> D-13125 Berlin
> Tel: 030-94793224
> Fax: 030-94793169
> mail: roeben at fmp-berlin.de
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