Hi Jason
So, if extra points do not work with the GB code how do you think i could compute the complex DeltaG considering the extra point. There is an easy to do that?
Thank you
Emilio
> Date: Thu, 5 Mar 2015 17:38:29 -0500
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] mm-pbsa & extra-point
>
> On Thu, Mar 5, 2015 at 4:42 PM, Emilio Angelina <
> emilioluisangelina.hotmail.com> wrote:
>
> > Dear Amber users/developers:
> >
> >
> > I ran MD simulations of protein-ligand complexes where the ligand has an
> > extra-point on an halogen atom to simulate the sigma hole. I did not have
> > problems to get the MD trajectories (actually I had faced a lot of issues
> > but I could solve it thank to your help).
> >
> > Now I want to compute the complex free energy with the mm-pbsa.py script
> > but it gives me very large values of the Van der Walls components. Is It
> > due to the extra-point? Could this have something to do with the fact that
> > there is no Van der Walls radius defined for the extra-point ? I have
> > pasted below part of the mm-pbsa output (see also the attach) so you can
> > see what I mean.
> >
>
> Extra points do not work with the GB code, but it should have given you an
> error (rather than running). I wonder if NAB doesn't have this check (or
> if it actually supports EPs...)
>
> That said, these numbers seem to be more caused by inconsistencies between
> the generated trajectories and the complex/receptor/ligand topology files.
> I would suggest visualizing these trajectories (_MMPBSA_complex.mdcrd.0,
> _MMPBSA_receptor.mdcrd.0, etc.) to see if they appear warped. If so, you
> need to double-check that you don't have any extra waters or anything in
> the complex or receptor topology files, and make sure that the topology
> files map correctly onto the trajectory files that are generated.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Mar 05 2015 - 16:30:03 PST
