[gmx-users] 1,5 and 1,6 LJ interactions for OPLS AA SEI

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 11 07:25:59 CEST 2011

> Hi everyone!
> The OPLS AA SEI for carbohydrates scales the 1,5 and 1,6 interaction 
> by a certain factor. How do I go about introducing the scaling of 
> these intearctions in the ff parameters? The CHARMM ff also has 
> certain 1,4 parameters, I am not sure how we can go about placing 
> these specific parameters in the ff.
> Your help is greatly appreciated. Thanks.

See use of fudgeQQ and nrexcl in section 5.7.1, and discussion of pairs 
and exclusions in 5.3.4 and 5.4. Basically you will want to exclude 1,5 
and 1,6 interactions with nrexcl and generate pair parameters by some 
mechanism. Different scalings for 1,4 1,5 and 1,6 would be a pain.

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