ff03 slightly favors alpha helix compared to ff99SB. since igb=5 favors
helix, I would not use them together. igb=7 seems to weaken most secondary
structure overall and in my opinion needs some refitting before extensive
production use.
the "best" combination depends on what you plan to do- is it for protein MD,
or just MM-GBSA postprocessing?
do NOT use ff94 or ff99 with GB, you will get only helix!
On Wed, Jun 3, 2009 at 6:28 AM, Andrew Voronkov <drugdesign.yandex.ru>wrote:
> Dear amber users,
> as far as the amber03 force field was parametrized with usage of
> electrostatic continuum models then it must be used with some correction
> parameters or not to be used at all with implicit solvent, right? I want to
> use amber03 with GBSA (igb=2 or 5 or 7) method and set up dielectric
> constant to 4 for the protein as was used in amber03 parametrization. Is it
> enough for usage of ff03 or it is better to use ff99 or ff94 with GBSA?
>
> Best regards,
> Andrew
>
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Received on Thu Jun 04 2009 - 01:07:59 PDT
