AMBER Archive (2009)

Subject: RE: [AMBER] ask for parm99MOD

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Thu May 28 2009 - 16:09:26 CDT

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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> >>>>>>>>> Associate Professor
> >>>>>>>>> Quantum Theory Project
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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
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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