Re: Namd with Amber ff for RNA minimization

From: Jérôme Hénin (
Date: Tue Nov 23 2010 - 02:14:20 CST

Dear Irina:

I am sorry to hear NAMD tried to change the structure of your DNA
helix - and apparently succeeded in doing so. Nevertheless, NAMD did
nothing but what you asked it to. It performed a local energy
minimization in vacuum, with a given force field. Now here are a
couple of questions:

- is that DNA fragment an A-helix in vacuum?
- is the force field _meant_ to give good results in vacuum?
- is the force field maybe meant to give solution structures when used
in vacuum?

I am by no means an expert on nucleic acids, but rumor has it that
they are sensitive to solvent effects, ionic strength and the like.


On 23 November 2010 07:43, Irina Tuszynska <> wrote:
> 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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:22 CST