Re: Namd with Amber ff for RNA minimization

From: Hannes Loeffler (Hannes.Loeffler_at_stfc.ac.uk)
Date: Tue Nov 23 2010 - 07:28:26 CST

I think the real question is why you want to minimise a highly charged
biomolecule in vacuo and expect it to keep a particular shape. I
highly doubt that the AMBER force field for nucleotides has been
parameterised for that purpose. What is the structure of RNA in vacuo,
anyway? Your result has probably no real physical meaning (and Jérôme
has hinted to that already).

Cheers,
Hannes.

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