thanks, I mean parm99.dat that was included in ff02. is this statement proper?
> From: carlos.simmerling.gmail.com
> Date: Thu, 28 May 2009 15:57:24 -0400
> Subject: Re: [AMBER] ask for parm99MOD
> To: amber.ambermd.org
>
> do you mean parm99 or ff02? these are different force fields. keep in mind
> that ff02 has many differences including charge model, so direct comparison
> is very difficult. comparison to ff99 is most direct but this is not a good
> force field. if you are talking about the protein force field that I think
> you are, it is a modification of something my lab published a while back. it
> was an early version of ff99SB, but had serious problems with Gly dihedrals,
> which
>
>
> On Thu, May 28, 2009 at 3:51 PM, xiaoqin huang <xqhuang1018.msn.com> wrote:
>
> >
> > yes, thanks, I want to test this parm99MOD2 on the protein I am simulating,
> > and compare with that of parm99.dat used in ff02.
> >
> > > From: carlos.simmerling.gmail.com
> > > Date: Thu, 28 May 2009 15:44:41 -0400
> > > Subject: Re: [AMBER] ask for parm99MOD
> > > To: amber.ambermd.org
> > >
> > > my personal opinion is that modifying backbone dihedral potentials to
> > > correct for problems in the solvent model is not going to be transferable
> > > among systems. also be very careful if you use this force field to
> > exactly
> > > math the GB model and radii to the ones used in the training.
> > >
> > >
> > > On Thu, May 28, 2009 at 3:41 PM, xiaoqin huang <xqhuang1018.msn.com>
> > wrote:
> > >
> > > >
> > > > sorry, I mean parm99MOD2, which is good for GB simulations.
> > > >
> > > >
> > > > > Date: Thu, 28 May 2009 15:38:23 -0400
> > > > > From: roitberg.qtp.ufl.edu
> > > > > To: amber.ambermd.org
> > > > > Subject: Re: [AMBER] ask for parm99MOD
> > > > >
> > > > > would you mind clarifyng what the parm99MOD is ?
> > > > > I have a suspicion that you refer to the hornak et al force field,
> > which
> > > > > would then can be found in amber as 99SB
> > > > >
> > > > > Adrian
> > > > >
> > > > >
> > > > >
> > > > > xiaoqin huang wrote:
> > > > > > got it, modify 4 torsional potentials.
> > > > > >
> > > > > >
> > > > > >
> > > > > >> From: xqhuang1018.msn.com
> > > > > >> To: amber.ambermd.org
> > > > > >> Date: Thu, 28 May 2009 14:16:35 -0400
> > > > > >> Subject: [AMBER] ask for parm99MOD
> > > > > >>
> > > > > >>
> > > > > >> hi, anyone can help me to find where is the parm99MOD set? I need
> > it
> > > > for GB simulations.
> > > > > >> thanks a lot
> > > > > >>
> > > > > >> xiaoqin
> > > > > >>
> > > > > >> 05/28/2009
> > > > > >>
> > > > > >>
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Received on Fri May 29 2009 - 01:13:08 PDT
