Article ID: 240 - Last Modified: December 4, 2010
Why is there a discrepancy between the vdW energies from oplsaa.vdw and the .mmo file?
The formula for the MacroModel non-bonded energy is
EVDW = 4.184*[CONST1/DISTANCE^12 - CONST2/DISTANCE^6]
First, MacroModel reports CONST1 and CONST2 in kcal/mol, but reports the EVDW values in kJ/mol, so there is a factor of 4.184 applied.
Second, the factor of 4.184 is the kcal to kJ conversion factor, not the normal factor of 4 in the LJ equation, which is included in the CONST terms.
Third, a factor of 1/2 must be applied for 1-4 interactions.
Fourth, the atom types shown in the connection table at the bottom of the .mmo file are MacroModel atom types, not OPLS vdW types. Therefore, the discrepancy might be due to looking up the wrong vdW parameters in the 'oplsaa.vdw' file. There isn't a simple way to get the OPLS vdW types/parameters. If you have MCPRO+, the easiest way is to run '$SCHRODINGER/utilities/ffld_server' with the '-print_parameters' option. Otherwise, you could run an Impact calculation with the keyword 'pparam' added to the "build types..." line in the jobname.inp file; a connection table with the OPLS vdW parameters will be printed to the .log file.
Keywords: atom types, macromodel, kcal, kJ, conversion factor
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