Dear Dr. Jason
Thanks so much for your interest and helpful reply.
If you don't mind, if there is a default value for the non-defined atoms, so why sometimes it complains and gives me "bad atom type" error?
One more question, sorry, is there any option to calculate molecular volume f the studied ligand. I spent all the last couple of days trying to find a way but I failed.
Thanks so much for your help
Eliac
--- On Sun, 3/20/11, Jason Swails <jason.swails.gmail.com> wrote:
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] MMPBSA question
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Sunday, March 20, 2011, 12:31 AM
> Hello,
>
> My comments are below:
>
> On Sat, Mar 19, 2011 at 4:35 PM, Eliac Brown <eliacbrown.yahoo.com>
> wrote:
>
> > Dear AMBER
> > I have been reading on MMPBSA and different
> methodologies for SASA
> > calculation.
> > As I am aware, MMPBSA.py reads the radii from the
> prmtop file, but the
> > written radii in the prmtop file is the effective born
> radii, and this is
> > different from the vdw radii which is needed in ICOSA
> calculation (after
>
>
> This is not quite accurate. Effective Born radii are
> recalculated
> throughout the simulation (every step unless you specify
> nrespa != 1).
> These are calculated via the coloumb field approximation,
> generally, which
> involves integrating over the volume of all other
> atoms. The radii stored
> in the prmtop file is *that* radius. While it's true
> that they are
> optimized for different GB models, they are not very far
> off of the VDW
> radii.
>
> augmentation by 1.4 for the solvent probe). So, how it
> comes?
> > On the other hand, using mmpbsa.pl version, ICOSA
> reads the radii from
> > compiled mdread file, but when I check the defined
> radii for chlorine in
> > mdread, I couldn't find it, and the program didn't
> complain, why? in other
> > case it complains such as in the case of zinc.
> > Any clarification would be appreciated.
> >
>
> If you look at line 1806 of mdread.f, you'll see that (for
> gbsa=1), the
> default atomic radii are set as 1.70 + the solvent probe
> radius (which is
> why you didn't get an error).
>
> Hope this clarifies things,
> Jason
>
> Thanks in advance
> > Eliac
> >
> >
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Mar 19 2011 - 18:00:04 PDT
