Dear Ton,
I am replying publicly, 'cause apparently there is no confidential
information in your letter, and it might be helpful for others to know.
First of all, it is just warning. Second, it directly indicates that
there is something wrong either with objective function - unrealistic
restraints produced by unrealistic template (with clashes for example)
or the structure at some point has become very unrealistic (again -
lotsa atom-atom clashes).
In my experience, it happened sometimes when I was using pseudoatoms
(for NMR-obtained restraints) or hydrogen models. Please also check if
the settings for topology model (TOPOLOGY_MODEL) and library (TOPLIB)
correlate with each other.
Hope this helps.
PS. It is just a warning.
Azat
Ton ter Laak wrote:
>
> Dear Azat,
>
> thank you very much helping us out with our
> stack limit. It helped ! The programm Modeller is running !
>
> But now we have loads of other error messages when running
> modeller. Do you recognize them ?
>
> chkder___W> DVZ(i) out of bounds: 214 214nan
> chkder___W> DVX(i) out of bounds: 216 216nan
> chkder___W> DVY(i) out of bounds: 216 216nan
> chkder___W> DVZ(i) out of bounds: 216 216nan
> chkder___W> DVX(i) out of bounds: 217 217nan
> chkder___W> DVY(i) out of bounds: 217 217nan
> chkder___W> DVZ(i) out of bounds: 217 217nan
> chkder___W> DVX(i) out of bounds: 218 218nan
> chkder___W> DVY(i) out of bounds: 218 218nan
>
> Thanks in advance,
>
> Ton ter Laak
--
- Azat Badretdinov, Ph.D.
- Molecular Simulations Inc.
- 9685 Scranton Road
- San Diego CA 92121-3752
- Phone: (858) 799 5728