Vsite parameters for DNA (AMBER)
There are no vsite parameters for the methyl group in thymine DNA. I have parameters for amber99sb-ildn that I could push. I have used them occasionally and successfully. In fact the only thing needed is the following constrainttype :
[ constrainttypes ]
MCH3 CM 2 0.166426
Also note that the DNA parameters are the same for several modern amber flavors.
So should I push them or is further testing required? Should I aim for 4-5-patches instead?