On Wed, Jun 13, 2007, mbrut.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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Received on Sun Jun 17 2007 - 06:07:13 PDT
