we need more information about "neutral terminals". do you mean a blocking
group so that both are neutral, corresponding to an experiment with the
termini acetylated and amidated? these are included as ACE and NH2. if you
mean you want to simulation an extreme pH and have 1 of the two termini
neutral, tell us that. it's not physical to have the N- and C-termini both
neutral in water without blocking groups.
On Tue, Mar 16, 2010 at 3:56 AM, Ramya Narasimhan <
ramyashree_81.rediffmail.com> wrote:
>
>
> I want to use the amber99sb force field in NAMD program to calculate the
> solvation interaction energy. I tried with top_amber_cornell.inp &
> par_amber_cornell.inp. But I want to have neutral terminals as in CHARMm. Is
> it possible to do so? If yes, can I get the details regarding this?
>
>
>
> Thanks for any comments/suggestions
>
>
>
> Ramya
>
> Ramya. L.
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>
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Received on Tue Mar 16 2010 - 04:00:02 PDT
