AMBER Archive (2009)

Subject: Re: [AMBER] Re: implicit solvent simulation with new ligand

From: Carlos Simmerling (
Date: Fri Aug 07 2009 - 13:29:46 CDT

I think in order to get a reply you need to be more specific in your
request. Did you try it and something did not work? The language is also a
bit confusing: "I there any problem" do you mean "would there be any
problem"? If there are no new atom types it should be fine. you might want
to look carefully at the intrinsic born radii that are assigned to your
ligand atoms and make sure they are reasonable. Since we don't know the
atoms or atom types, it is hard to make specific comments I think you will
need to try it out and see what happens. As always, make sure you are either
very experienced, or following something from the peer-reviewed literature
that successfully performed the kind of study that you want to do. For
example, with igb=5 you still need to select the intrinsic radii in leap.

On Fri, Aug 7, 2009 at 2:22 PM, Manish Kumar <>wrote:

> Dear Experts,
> I am anxiously waiting for any reply.
> Sincerely,
> Manish
> On Thu, Aug 6, 2009 at 11:29 PM, Manish Kumar <
> >wrote:
> > Dear Expert,
> >
> > My this query is actually a follow up of the last post.
> >
> > I have parameterized my ligand using RED, and my parameters does not have
> > any new atom type. I there any problem in running simulation in implicit
> > solvent with this ligand using igb=5.
> >
> > Sincerely,
> > Manish
> >
> >
> >
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