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 >