Thanks for the advice.
Since we only have Amber7 available, I might have to use the old parm94.
Do I still need to neutralize the entire system before subject to MD?
Thank you.
Bo
On Mon, 30 Aug 2004 09:41:21 -0400 Carlos Simmerling wrote:
> we and others have published articles showing that parm99
> strongly overstabilizes alpha-helical conformations. on the ns-timescale
> things may be ok, but over longer periods the protein becomes
> more helical. folding studies with parm99 are likely worthless.
>
> there are several parm94 variants that have been published in the past
> few years. we published a change in 2002, Angel Garcia uses a
> different modification, and so on. AMBER8 includes a few of these.
> carlos
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Assistant Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
> ===================================================================
>
>
>
>
> Chris Harrison wrote:
>
> > Could you please explain why parm99 is unsuitable for protein
> > simulations and if so, what forcefield would be suitable for protein
> > simulations?
> >
> > Chris
> > charris5.nd.edu
> >
> >
> >
> > Carlos Simmerling wrote:
> >
> >> parm99 is probably not a good choice for protein simulations.
> >>
> >> ===================================================================
> >> Carlos L. Simmerling, Ph.D. Assistant Professor Phone:
> >> (631) 632-1336 Center for Structural Biology Fax: (631) 632-1555
> >> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> >> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
> >> ===================================================================
> >>
> >>
> >>
> >>
> >> bybaker.itsa.ucsf.edu wrote:
> >>
> >>> Hello, Amber:
> >>>
> >>> I am planning to run MD on my protein structure model under
> >>> physiological (pH 7.0) and acidic (i.e. pH 4.0) conditions. In order
> >>> to mimic the low
> >>> pH condition, all Asp, Glu and His residues in the model will be
> >>> changed
> >>> to their protonated states. After the changes, the net charge of the
> >>> structure is +32. Should I neutralize the structure by ‘addIon2’
> before
> >>> any energy minimizations, or just leave it without adding Cl- ions ?
> >>>
> >>> I use Amber7 with ff.99 force field.
> >>> Thanks advance.
> >>>
> >>> Bo
> >>>
> >>>
> >>>
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Received on Thu Sep 02 2004 - 01:15:12 PDT
