Re: How to avoid funny structure in all-hydrogen modeling?
To: Lesheng Kong <>
Subject: Re: How to avoid funny structure in all-hydrogen modeling?
From: Bozidar Yerkovich <>
Date: Wed, 21 Aug 2002 10:31:43 -0400 (EDT)
Cc: "''" <>
refine_5 is the most extensive MD optimization, not refine_1 ;-)
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