Re: How to avoid funny structure in all-hydrogen modeling?

[Bozidar Yerkovich <bozidar@salilab.org>]

refine_5 is the most extensive MD optimization, not refine_1 ;-)

Bozidar

On Wed, 21 Aug 2002, Lesheng Kong wrote:

> Dear all,
> Have anyone ever generated all-hydrogen models?
> For all-hydrogen modeling, the generated models always have some funny 
> structures(such as one hydrogen atom is connected with several other atoms. I 
> think some maybe due to bad contact, but some bond lengths are longer than 
> 2.5 angstrom). These funny connections sometimes appear in ARG and SER. 
> Is it possible because models have not been thoroughly refined? I have tried 
> to set MODELLER "MD_LEVEL" to "refine_1" (# very thorough MD optimization), 
> but no effects.
> How to avoid or remove these funny structures in all-hydrogen modeling?
> Thank you very much for your kind help! 
> With best regards,
> Kong Lesheng
>