AMBER Archive (2009)

Subject: Re: [AMBER] ask for parm99MOD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 28 2009 - 14:57:24 CDT

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_at_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_at_gmail.com
> > Date: Thu, 28 May 2009 15:44:41 -0400
> > Subject: Re: [AMBER] ask for parm99MOD
> > To: amber_at_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_at_msn.com>
> wrote:
> >
> > >
> > > sorry, I mean parm99MOD2, which is good for GB simulations.
> > >
> > >
> > > > Date: Thu, 28 May 2009 15:38:23 -0400
> > > > From: roitberg_at_qtp.ufl.edu
> > > > To: amber_at_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_at_msn.com
> > > > >> To: amber_at_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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