Hello,
You did not specify which version of Amber you're using, so I'm going to
respond for the case of Amber11 and AmberTools 1.4. One thing that you can
try to do is increase cutres to something like 999 in the _MMPBSA_pb.mdin
input file (use the -make-mdins and -use-mdins flag as described in the
manual). In pb_init.f ($AMBERHOME/AmberTools/src/pbsa), maxnbr is set to
maxnbr_l = dble(natom) * ( sqrt( cutres ) + 3.0d0 )**3 / 3.0d0
So it would seem to me that increasing cutres will make maxnbr_l (which is
set to maxnbr if natom**2 is not too large). Note that maxnbr takes on the
smaller of the 2 values between the above value and
1/2 natom ** 2
If the latter is the limiting value (you can calculate these values pretty
easily just by plugging in your number of atoms and desired value of cutres,
such as 999), than you can edit the source code and possibly take out the
factor of 1/2 by changing the line
maxmax = ceiling(dble(natom)/2*dble(natom))
to
maxmax = ceiling(dble(natom)*dble(natom))
in the pb_init.f file I described above. You'll have to recompile
afterwards of course (both pbsa and sander if you compiled with static
libraries).
Perhaps one of the PBSA developers can give you a better answer...
Good luck!
Jason
On Thu, Aug 19, 2010 at 12:55 AM, Wookyung Yu <sfcywk.gmail.com> wrote:
> Dear AMBER users.
>
> I did MD simulation using a large protein which has about 3000 amino acids.
>
> I want to use MMPBSA.py but this gives error message.
>
> " PB bomb in pb_reslist(): maxnbr too small "
>
> How do I overcome this error message?
>
> Thanks in advance.
>
> Wookyung Yu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 18 2010 - 23:30:04 PDT
