i suggest making a prmtop just for the ligand, then it is small enough that
you can look at the prmtop and see the radii.
On Fri, Aug 7, 2009 at 3:08 PM, Manish Kumar <kumarmanish.amb.gmail.com>wrote:
> 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
> > > >
> > > >
> > > >
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Received on Wed Aug 19 2009 - 21:17:49 PDT
