Thanks for the reply.
Sorry for the typing mistakes in my first mail. I meant to write "Is there
any problem". And by problem I mean consistency issues like having correct
born radii assigned to every atom etc.
How can I look and compare the born radii?
And for igb=5, Used "set default PBradii mbondi2" in tleap.
I want to calculate mm-gbsa free energy of binding of my ligand (which has
been parameterized) by running simulation in implicit solvent.
Sincerely,
On Fri, Aug 7, 2009 at 2:29 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 <kumarmanish.amb.gmail.com
> >wrote:
>
> > Dear Experts,
> >
> > I am anxiously waiting for any reply.
> >
> > Sincerely,
> > Manish
> >
> > On Thu, Aug 6, 2009 at 11:29 PM, Manish Kumar <kumarmanish.amb.gmail.com
> > >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
> > >
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 20:57:56 PDT
