Hi,

I just wanted to know if there is a scaling rule applied for determining the van der Waal parameters (sigma and well depth of carbonyl oxygen and aliphatic carbon in acetic acid) for the 1-4 non-bonded interactions. I know that for OPLS-AA force field, the potential parameters are scaled by 1/2, for 1-4 non-bonded interactions.

Thanks

Ganesh

1,4 scaling can be done for both electrostatic and LJ terms. In charmm
1,4 scaling of electrostatics is NOT done (i.e. scale factor = 1); the
corresponding value is OPLS is 1/2 or 1/1.2. LJ or VDW 1,4 scaling
is typically done for a particular atom type by inclusion of 3 additional
columns (alpha, epsilon, Rmin) to the Nonbond section of the
parameter file; example are already in the charmm22 protein
parameters. Note that such scaling is only applied in special
cases; an alternative would be to add an off-diagnol LJ interaction
term for the 2 atom types of interest via the NBFIX section of
the parameter file.

alex


alex