The article on parm99 (Wang, Cieplak and Kollman, J Comp Chem 2000)
the changes that were made. Most were for organic functional groups,
but some of these changes are applied to protein side chains.
The protein phi/psi backbone parameters were also changed. You can't
really read any importance into the change you see in absolute dihedral
energy; what matters is the relative energies between conformations
using the same force field. In other words, the zero of energy doesn't
matter. I don't think anyone has published a study comparing the relative
behavior of protein/RNA complexes with the two parameter sets.
carlos
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================
----- Original Message -----
From: "Vlad Cojocaru" <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
To: "amber list" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, August 27, 2002 9:34 AM
Subject: difference 94 99 force field
> One of the past days I posted a message asking about differences between
> the 2 force fields. Now I have done 2 simple minimizations using amber6
> with both 94 and 99 force field on an 33 nucletides RNA and on a 104
> residues protein. The sander input file is given below.
> The differences in the output file from snader are seen only at Dihedral
> term. All the rest is basically the same. In the case of protein the
> value of the dihedral almost doubled while in the case of RNA the
> increase is not that significant (as values I can say that for the
> protein DIHED = ~450 with 94 ff and =~ 930 with 99 ff and for the RNA
> ~620 with th 94 ff and ~730 with 99ff.
> I also have to say that the structures from both minimization are
> almoost perfectly identical (rmsd =0.1319 for the protein and 0.061 for
> the RNA)
> Could somebody shortly describe the reasons for this behavior...or point
> me to some references so that i can figure it out myself? What one would
> expect for an MD?
> Thanks a lot for any advices and possible Replies.
> Best regards,
> vlad
>
> &cntrl
> imin=1, ntf=1, igb=3, dielc=4.0, cut=25., ntr=1,
> scnb=2.0, scee=1.2, ntb=0,
> maxcyc=10000, ncyc=50, ntmin=1, dx0=0.001, dxm=0.05,
> drms=0.05, dele=0.000001
> &end
> Constraints 20 [kcal/mol]
> 20.0
> RES 1 105 (33 for RNA)
> END
> END
> DasEnde
> (the same script wa applied with 15, 10, 5, 1, 0.1 and 0 constraints)
>
> --
> Vlad Cojocaru
> Max Planck Institut for Biophysical Chemistry
> Deparment: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>
>
>
>
Received on Tue Aug 27 2002 - 07:34:50 PDT
