positive lennard Jones energies

[Michael Nilges]

Jane,


The Lennard Jones energies depend very much on the force field, and the
exact parametrization of the nonbonded interaction, including  
electrostatics.
Positive vdW energies can, however, indicate that your NOEs might  
be a little
tight, or that the final REPEl value is a little low. We are using  
REPEl=0.78
with good results.

You can also refine with a ``normal'' non-bonded
representation. I would suggest to do this keeping the rigid geometry 
of parallhdg. To do this, you can replace the non-bonded section
in parallhdg with the values from parmallh6 given below. For the  
electrostatics,
I would use   RDIEL, EPS=4; or RDIEL, EPS=1 and a reduction of all  
charges of
formally charged residues to 1/3. The charges in topallhdg are from  
topallh6, so
the non-bonded representation would be self consistent. parmallh6  
has an explicit
hydrogen bond potential. The following setup can be used also  
simply for an analysis
of your structures - print hbond will give you a list of all  
hydrogen bonds.

parameter
  nbonds
    nbxmod=5 group rdiel switch vswitch
    cutnb=10.0 ctofnb=9.0 ctonnb=5.0 eps=4.0 e14fac=0.4
    wmin=1.5    tolerance  0.5
  end
  hbonds
    aexp=4  rexp=6  haex=4  aaex=2  acceptors true
    DCUT= 5.0 DOFF= 4.0 DON= 3.5
    acut=90.0 aoff=70.0 aon=50.0
  end
end
flags include hbond end


A little more expensive but still feasible is a refinement with  
full electrostatics
in explicit solvent, also using the rigid geometry of parallhdg.  
This would avoid the
artefacts of using lennard-jones and electrostatics in vacuo.


Michael.

REMARKS non-bonded values from parmallh6 for use with parallhdg

 nonbonded  C       0.0903   3.2072      0.0903   3.2072
 NONBonded  CA      0.0903   3.2072      0.0903   3.2072
 NONBonded  CB      0.0903   3.2072      0.0903   3.2072
 NONBonded  CC      0.0903   3.2072      0.0903   3.2072
 nonbonded  CH      0.0903   3.2072      0.0903   3.2072
 NONBonded  CN      0.0903   3.2072      0.0903   3.2072
 NONBonded  CP      0.0903   3.2072      0.0903   3.2072
 NONBonded  CR      0.0903   3.2072      0.0903   3.2072
 nonbonded  CT      0.0903   3.2072      0.0903   3.2072
 NONBonded  CV      0.0903   3.2072      0.0903   3.2072
 NONBonded  CW      0.0903   3.2072      0.0903   3.2072
 NONBonded  CX      0.0903   3.2072      0.0903   3.2072
 nonbonded  H       0.0498   1.4254      0.0498   1.4254
 nonbonded  HA      0.0045   2.6157      0.0045   2.6157
 nonbonded  HC      0.0498   1.4254      0.0498   1.4254
 nonbonded  N       0.1592   2.7618      0.1592   2.7618
 NONBonded  NA      0.1592   2.7618      0.1592   2.7618
 NONBonded  NB      0.1592   2.7618      0.1592   2.7618
 nonbonded  NC2     0.1592   2.7618      0.1592   2.7618
 nonbonded  NH1     0.1592   2.7618      0.1592   2.7618
 nonbonded  NH2     0.1592   2.7618      0.1592   2.7618
 nonbonded  NH3     0.1592   2.7618      0.1592   2.7618
 nonbonded  O       0.2342   2.6406      0.2342   2.6406
 nonbonded  OC      1.0244   2.6406      1.0244   2.6406
 nonbonded  OH      0.2342   2.6406      0.2342   2.6406
 nonbonded  QA      0.0045   1.0000      0.0045   1.0000
 nonbonded  QC      0.0045   1.0000      0.0045   1.0000
 nonbonded  QH      0.0045   1.0000      0.0045   1.0000
 nonbonded  S       0.0239   3.3854      0.0239   3.3854

!                   Emin      Rmin
!                (Kcal/mol)   (A)
hbond NA   N%      -3.00      3.0!  VALUES FROM VINOGRADOV AND LINELL FOR
hbond N*+* N%      -3.00      3.0!  VALUES FROM VINOGRADOV AND LINELL FOR
hbond NA   O*      -3.50      2.9!  TYPICAL LENGTHS AND DEPTHS.
hbond N*+* O*      -3.50      2.9!  TYPICAL LENGTHS AND DEPTHS.
hbond OH*  N%     -4.00      2.85
hbond OH*  O*      -4.25      2.75
hbond S    N%      -3.00      3.0 !! added, ATB
hbond S    O*      -3.50      2.9 !! added, ATB