igb=8 is a much improved igb=7 model. I don't recommend using the original
igb=7. However, at this point we have not released improved parameters for
igb=8 for nucleic acids- these are in progress. I don't recommend igb=7 for
your system. You might try igb=1, but be careful and make sure to try to
find similar studies in the literature and follow their method. if you
can't find similar studies, be aware that you will have to proceed with
caution and find a way to validate your work against experiment.
On Tue, Sep 4, 2012 at 11:41 AM, jit mukherjee <jitiitkgp.gmail.com> wrote:
> Dear Amber Users,
> I want to use igb=7 in the input file as it better describe the real
> situation more accurately and is nearly equivalent to the explicit solvent
> model. But it is mentioned in the Amber 9 user Manual that this model is
> not recommended for systems involving nucleic acids.
> Now, my system is a carbon nanotube system functionalized with nucleic acid
> base, e.g., adenine. Can I use the igb=7 gb model?
>
> Regards,
> jit
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Received on Tue Sep 04 2012 - 09:00:06 PDT
