AMBER Archive (2009)

Subject: RE: [AMBER] ask for parm99MOD

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Thu May 28 2009 - 14:51:59 CDT


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.
> > > >>
> > http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009_______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER_at_ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > > _________________________________________________________________
> > > > Hotmail® has a new way to see what's up with your friends.
> > > >
> > http://windowslive.com/Tutorial/Hotmail/WhatsNew?ocid=TXT_TAGLM_WL_HM_Tutorial_WhatsNew1_052009_______________________________________________
> > > > AMBER mailing list
> > > > AMBER_at_ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > > --
> > > 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
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _________________________________________________________________
> > Windows Live™: Keep your life in sync.
> >
> > http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009_______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_________________________________________________________________
Hotmail® has a new way to see what's up with your friends.
http://windowslive.com/Tutorial/Hotmail/WhatsNew?ocid=TXT_TAGLM_WL_HM_Tutorial_WhatsNew1_052009_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber