AMBER Archive (2008)

Subject: Re: AMBER: Antechamber and topology file

From: David A. Case (
Date: Thu Jun 12 2008 - 11:03:50 CDT

On Wed, Jun 11, 2008, TAEJIN KIM wrote:
> I placed this modified nucleotide into
> larger RNA structure which has 46 residues and problem happened when
> I ran the MD. The structure was getting unstable as time goes on, and
> C3' endo of most residues changed to C2' endo, which is hard to
> believe to happen in RNA.

The torsional parameters for RNA have been hand-developed with a eye toward
giving a good pseudo-rotational profile for the sugar. There is certainly no
guarantee that just applying a completely general force field would preserve
such (fairly) fine distinctions.

You might want to consider starting from Adenine, and hand-modifying files to
create your modified nucleotide (is the modification in the base?) That way,
the sugar and backbone parameters would be the same as for the regular bases.
Antechamber could be used to get estimates of some of the parameters you might

...good luck....dac

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