AMBER Archive (2004)

Subject: Re: AMBER: question about NMODE for RNA

From: David A. Case (case_at_scripps.edu)
Date: Sun May 30 2004 - 18:14:33 CDT

On Sun, May 30, 2004, xhu1_at_memphis.edu wrote:
>
> I am trying to run NMODE for RNA. SANDER is used to carry out
> conjugate gradient minimization. Due to the large electrostatic
> repulsion force between two chains, I minize the RNA in implicit
> solvent using GB option(igb=1), which outputs an energy item
> called "EGB", and includes this energy in the total enegy calculation.
> But in NMODE program, there is no GB option. EGB will not be included
> so that the good RMSD values gotten from minimization is lost.

This is correct. We are working on getting second derivatives for the GB
energy function, but this is not yet completed. The general workaround
(by no means completely satisfactory) is to minimize with epsilon=4r
(that is, dielc=4 and eedmeth=5), then use that also for normal modes.
It is not well established yet how good or bad an approximation this is.

...good luck...dac

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