AMBER Archive (2007)

Subject: AMBER: Hbonds

From: mbrut_at_laas.fr
Date: Thu Jun 14 2007 - 02:45:25 CDT

Thank you David,
I see what you mean...
I did that because I found a message in the archive :

> 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.

And your answer :

> 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.

isn't it possible, but with igb=0 ?

Thanks again,

Marie

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