AMBER Archive (2009)

Subject: RE: [AMBER] ask for parm99MOD

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Thu May 28 2009 - 15:32:02 CDT

I use ff02, but parm99.dat is loaded into xleap when source leaprc.ff02. I want to see the difference between parm99.dat and parm99MOD2 for my protein when using the same PBradii mbondi2. According to the reference of GB-OBC model, the parm99MOD2 is better.

> From: carlos.simmerling_at_gmail.com
> Date: Thu, 28 May 2009 16:22:31 -0400
> Subject: Re: [AMBER] ask for parm99MOD
> To: amber_at_ambermd.org
>
> no- do you mean ff99 or ff02? they are different force fields.
>
> On Thu, May 28, 2009 at 4:09 PM, xiaoqin huang <xqhuang1018_at_msn.com> wrote:
>
> >
> > thanks, I mean parm99.dat that was included in ff02. is this statement
> > proper?
> >
> >
> >
> > > From: carlos.simmerling_at_gmail.com
> > > Date: Thu, 28 May 2009 15:57:24 -0400
> > > Subject: Re: [AMBER] ask for parm99MOD
> > > To: amber_at_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_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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