[gmx-users] adding new residue (MSE) in topology database

[Mark Abraham]

anwar at cdfd.org.in wrote:
> hello,
> I am trying to add Selenomethionine (MSE) residue in to the topology 
> database. And I have to calculate the van der waals parameters V(c6)
> and W(c12) as they have to be mentioned in ff???nb.itp, for which I
> have to get the sigma and epsilon values. Where can I find these
> valuse or how can I calculate them.

Find the papers that described the development of the forcefield you are 
trying to extend and see how they developed these parameters. Then try 
and do something consistent with that.

Mark