Re: Namd with Amber ff for RNA minimization

From: Irina Tuszynska (
Date: Tue Nov 23 2010 - 05:29:33 CST

Dear Jerome,

Thank you for your respond and suggestions. But I have performed
minimization for RNA not DNA. Native RNA molecules have A-type helix.
Next, as far as I know all parameters in Amber are taken from small
molecules QM simulations in vacuum (please tell me if I am wrong).
So maybe there should be some parameters to keep a structure for example
DNA in B-type helix while RNA in A-type helix. Perhaps I should turn on
any function in NAMD to say that it is RNA?


Jérôme Hénin wrote:
> 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.
> Best,
> Jerome
> 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.

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