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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Received on Sun Feb 24 2013 - 07:00:03 PST
