AMBER Archive (2009)

Subject: RE: [AMBER] ask for parm99MOD

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Thu May 28 2009 - 16:43:15 CDT

ok, I give up comparison, and could you help to tell me the published comparisons, and also papers on minor weakness of GB-OBC model?

> From: carlos.simmerling_at_gmail.com
> Date: Thu, 28 May 2009 17:17:05 -0400
> Subject: Re: [AMBER] ask for parm99MOD
> To: amber_at_ambermd.org
>
> 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
> > > >>>>>>>>>>>
> > > >>>>>>>>>>>
> > > >>>>>>>>>>>
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> > > >>>>>>>>>
> > > >>>>>>>>> Senior Editor. Journal of Physical
> > > >> Chemistry
> > > >>>>>>>>> American Chemical Society
> > > >>>>>>>>>
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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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