[gmx-users] Topology builder

[Mark Abraham]

> Dear Mark,
>
> The problem is a little bit more complicated. I want to build topologies
> for
> dozens of non-peptide inhibitor prototypes using OPLS FF. Thus, if there
> is a
> way to build this by an automatic procedure it would save much time.

Well, if there was one, I might have mentioned it before :-)

The difficulty is that assignment of atom type to arbitrary chemical
species is a tricky pattern-recognition problem. Still, this must be
something that programs like Autodock have to deal with, so you should
have a look at such docking programs and see what they do.

Otherwise, you could write such a program... :-)

Mark