[gmx-users] pairs in OPLS

[Lars Schaefer]

Hi all,

I've just a simple question concerning OPLS topology: If I have defined 
a Ryckaert-Bellemans dihedral angle between, say, atoms 1-2-3-4, do I 
have to add the atoms 1 and 4 also to the [ pairs ] list nevertheless? 
The manual says:

"If you want to include Ryckaert-Bellemans type
dihedrals in a topology, do the following (in case of e.g. decane):
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
1 2 3 4 3
2 3 4 5 3
and do not forget to erase the 1-4 interaction in [ pairs ]!! "

So I think I do NOT have to add my atoms 1 and 4 to the [ pairs ] list. 
But pdb2gmx does it...
Does the manual in this respect perhaps refer to e.g. the GROMOS force 
fields only?

Thanks in advance, Lars


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Lars Schaefer
MPI fuer biophysikalische Chemie