Jason K wrote:
>
> So far I've been running everything using ff99, but I have been
> thinking for several months it may be worth switching to "better"
> parameter sets.
>
yes, you need to switch NOW. ff99 should not be used, in my opinion.
Use ff99SB or ff03 (both are good, but different charge models).
ff99 has very serious problems and my feeling is that anything
published using it should be very carefully checked. new work using
ff99 should probably not be published. again, that's just my opinion but
there is a lot of evidence to back it up and problems with ff99 have
been published now for years so there's no reason anyone should
have been using it in their recent studies.
> If not, could someone point me to the direction of performing MD or
energy minimisation using internal coordinate restraints? > Are the
options used the same used for NMR-type restraints?
yes, you can use NMR restraints for this. we have done that.
I can't help on your other questions.
good luck!
carlos
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Received on Wed Jan 31 2007 - 06:07:10 PST
