[gmx-users] Energy minimization: problems with ramachanrad score

[marcos]

Perhaps this can help you

Christopher M. Summa and Michael Levitt
Near-native structure refinement using in vacuo energy minimization
PNAS 2007 104: 3177-3182; published online before print as 
10.1073/pnas.0611593104 


Marcos

On Wed, 2007-04-25 at 14:46 +0400, dimitry.a.suplatov wrote:
> Hello.
> I'm doing homology modeling. My model after MODELLER has Ramachandran
> Z-score = 0.7 (that is OK). Then Im doing energy minimization with
> steep, emtol=200 KJ/mol*nm. Fmax was converged to 1.82684e+02 in about
> 4000 steps. Backbone RMS compared to MODELLER model is 0.27nm. Z-score
> is -3.5 and that is very poor.
> Questions:
> 1. Could 4000 steps be too much for minimization? May be I should use
> not more than 1000 and do not care about Fmax?
> 2. What minimization protocol do you prefer? What about using different
> alorythms step by step?
> 
> Thank you.
> Dimitry. 
> 
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