From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Fri Jan 23 2009 - 16:30:16 CST
Hi everybody
Many thanks for all this valuable information.
Certainly I did not expect the parametrization of a new molecule to be a ride in the park ! That is why I thought it appropriate to ask first the opinon of wise men instead of rushing boldly in the wrong direction....and hopefully I'll limit the potential damage to myself.
Now it's clear to me that the splitting of the larger cycle (80 atoms) of the molecule is unavoidable and that I have to 'squeez' more computer power from my university. Probably I will do the first learning trials on the 'piunny little' machine mentioned and than I will try to snatch some time on the Linux cluster which is foreseen to be installed at our site.
But still it is not clear for me if simulations with NAMD using CHARMM22 would be more appropriate with CHARMM or AMBER charges. In Paratool documentation it is explain how to derive them but not if one or the other would be more appropriate in a certain context.
Best wishes
Vlad
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