AMBER Archive (2007)

Subject: Re: AMBER: Hbonds

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 13 2007 - 15:50:11 CDT

On Wed, Jun 13, 2007, mbrut_at_laas.fr wrote:

> I try to minimize a DNA-dodecamer with SANDER in implicit solvent,
> and then to make a normal mode analysis with NMODE.

This will never work, since nmode doesn't know about generalized Born
solvation. You could look at NAB (http://www.scripps.edu/case) -- of course
at the expense of learning a different program.

> igb = 1,
> dielc = 4,

This won't work. It could be that combining "dielc" with igb=1 is causing
your structure to fall apart. Setting dielc to anything other than its
default value of 1 is very dangerous for nucleic acids.

...good luck...dac

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