Namd with Amber ff for RNA minimization

From: Irina Tuszynska (irena_at_genesilico.pl)
Date: Tue Nov 23 2010 - 00:43:56 CST

Dear All,
I have run minimization of a RNA in vacuo with help of Amer force field
in NAMD. But at the end of minimization I have rather had B-helix
instead of A(it was A at the beginning of the simulation)? I should say
that parametrization was ok, because Amber ff recognized ribose and
uridine properly, but why NAMD try to change the type of helix?
I would be grateful for any help.

Best,
Irina.

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