This error is a result of the number of non-bonded residues being too small
because cutres is too small. We have seen this error occur, but usually only
for fairly large systems. In this situation, I would suggest using the
-make-mdins flag with MMPBSA.py to make all of the mdins that the program
will use to run sander, and then edit the pb input file that was created
(_MMPBSA_pb.mdin) and set cutres in the &pb section to a larger number. The
default is 99, so try something larger than that (i.e. 999). Then use the
same command you would have originally, but then add the flag -use-mdins at
the end so that the script will use the input files that it already made
with your edit(s).
To answer your second question, the best relationship between delta G and
the equilibrium constant is
delta G = -RT ln K
However, although this does relate delta G and the equilibrium constant,
remember that K does not have units in this equation since you can not take
the log of something that has units.
Good luck!
-Bill
On Tue, May 25, 2010 at 9:54 AM, Chanchal <chanchal.kar.gmail.com> wrote:
> Hi all,
> I am trying to estimate the binding free energy of a ligand (steroid) to
> a protein using MMPB/SA & MMGB/SA approaches. I am using MMPBSA.py
> available in amber 11. I followed the amber tutorials. My GB calculation
> was
> successful but the PB calculation failed. The ourput of the
> _MMPBSA_complex_pb.mdout & _MMPBSA_receptor_pb.mdout shows the following
> error message:
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> trajectory generated by
> ptraj
> minimizing coord set # 1
> PB bomb in pb_reslist(): maxnbr too small
>
> Please let me know how can I fix this error.
>
> 2. I have another naive question. I got binding free energy (delta G) from
> MMGB/SA calculation. Now I want to estimate the binding affinity in nM
> unit.
> How can I do it?
> Thanks
> Chanchal
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 25 2010 - 07:30:11 PDT
