AMBER Archive (2002)

Subject: difference 94 99 force field

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Tue Aug 27 2002 - 08:34:11 CDT

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