Yes, I want to calculate the total binding free energy of protein with both
ATP and Mg2+. I have already merged the files of Mg and ATP in one file
(the ligand file). But when I have tried to run MMPBSA, it gives an error
during "calculating ligand contribution". So, I need suggestion/help to
overcome this problem.
Jason,
Thanks for your advise regarding netiquette. I would definitely remember
that.
Saugata
On Sun, Feb 24, 2013 at 9:43 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sat, Feb 23, 2013 at 7:51 PM, Saugata Hazra <saugata.iitk.gmail.com
> >wrote:
>
> > Thank you very much Alessandro for your reply. I guess you are right
> > regarding this prmtop problem.
> > The problem arises probably because of the fact that I had a metal (Mn2+)
> > included with the protein.
> > Now after taking out the metal, the ba2291_prot.prmtop file is finally
> > running.
> >
> > But now I have to treat Mn2+ as a ligand, so I have two ligands ( one is
> > ATP and another is Mn2+ ion). There is option of only one ligand and a
> > merged file including both is not running.
> > Any further suggestion!!!!!!!!!!!!
> >
>
> You will have to divide this into two steps. MM/PBSA calculates a binding
> free energy for non-covalent binding of _a_ ligand with _a_ receptor. How
> you treat a system with two ligands depends on what you want to learn, but
> you will have to divide your system into a single ligand (e.g., ATP, Mg2+,
> ATP+Mg2+) and a single receptor. Basically, the Mg ion will either need to
> be part of the ligand or part of the receptor, and the same goes with ATP.
>
> Do you want to look at the total binding free energy of both ATP and Mg?
> Then the `ligand' should be both. Do you want to look at how well ATP
> binds when Mg is bound in the protein? Then the Mg should be part of the
> `receptor'.
>
> As a side note, it's typically considered good netiquette to either avoid
> using exclamation points or to use only one (for the same reason you should
> avoid sending emails in all caps -- it gives the impression of shouting).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
--
*Know me Know fun, no me no fun!!!*
Dr. Saugata Hazra
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Received on Mon Feb 25 2013 - 11:00:03 PST
