AMBER Archive (2009)

Subject: Re: [AMBER] ask for parm99MOD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 28 2009 - 15:52:56 CDT

I see- I think you need to check with Alexey Onufriev but that may have been
an early version of ff99SB.
read the ff99SB paper to see the differences between ff99 and ff99SB. do not
use ff02 or anything related- you'll get confused, since that has little to
do with ff99.
if you want to comapre ff99 and ff99SB, use those files in leap. don't use
ff02 unless that is really what you want.

On Thu, May 28, 2009 at 4:32 PM, xiaoqin huang <xqhuang1018_at_msn.com> wrote:

>
>
>
>
>
>
>
> 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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