Thank you, Dr. Case! I see.
regards
Shawn
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
Date: Monday, May 31, 2004 7:14 am
Subject: Re: AMBER: question about NMODE for RNA
> On Sun, May 30, 2004, xhu1.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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Received on Mon May 31 2004 - 03:53:00 PDT
