AMBER Archive (2009)

Subject: Re: [AMBER] ask for parm99MOD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 28 2009 - 16:17:05 CDT

unless you have a reason to think about ff02, don't involve it any more.
it's not related to the Onufriev paper and not related to ff99.
if you want to know about ff02, then we can talk about that.
for the paper you mentioned, it was an early version of ff99SB but had some
weaknesses, especially in glycine, which we improved later in ff99SB.
ff99SB is what I suggest that you use. ff99 is very bad, please don't use it
unless you want to know something specific, but not to learn anything about
proteins.
also unless you want to do comparisons yourself, I suggest checking the
literature because many comparisons have already been published.
if you just want to run the best simulation that you can, I suggest ff99SB
(but be careful with GB, the GB-OBC model is very good but does have a few
minor weaknesses that have also been reported in the literature).

On Thu, May 28, 2009 at 5:09 PM, xiaoqin huang <xqhuang1018_at_msn.com> wrote:

>
> does this mean the parm99MOD2 is only good for ff99SB, and not necessary to
> change that four torsional potentials in ff02, right?
>
>
>
> > Date: Thu, 28 May 2009 16:56:14 -0400
> > From: roitberg_at_qtp.ufl.edu
> > To: amber_at_ambermd.org
> > Subject: Re: [AMBER] ask for parm99MOD
> >
> > HI all,
> > I just re-read the Proteins paper you sent to all.
> > Indeed, the parmmod2 used there was the one used to fold trp-cage.
> > As carlos mentioned, this is an early version of ff99SB.
> >
> > Use ff99SB and you should be fine.
> > Adrian
> >
> >
> > Carlos Simmerling wrote:
> > > 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
> > >>>>>>>>>>>
> > >>>>>>>>>>>
> > >>>>>>>>>>>
> > >>>> _________________________________________________________________
> > >>>>>>>>>>> Windows Live™: Keep your life in sync.
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> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project
> > Department of Chemistry
> >
> > Senior Editor. Journal of Physical Chemistry
> > American Chemical Society
> >
> > University of Florida PHONE 352 392-6972
> > P.O. Box 118435 FAX 352 392-8722
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