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Re: Modeller



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