Try visualizing the ligand trajectory (_MMPBSA_ligand.mdcrd) with your
ligand prmtop file to make sure that they're compatible. You should also
try running PB calculations on the ligand alone to see if it works outside
of MMPBSA.py.... I'm not sure exactly what's happening here.
Did you apply all bug fixes?
Good luck!
Jason
On Tue, Oct 5, 2010 at 8:06 PM, Anuradha Mittal
<anuradha.mittal.gmail.com>wrote:
> Hi,
>
> I am doing the free energy calculations using MMPBSA with Amber11
> (mmpbsa.py), but I am getting the following error for the ligand.
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> trajectory generated by ptraj
> minimizing coord set # 1
> PB warning in pb_miccg(): CG l_maxitn exceeded!
> PB warning in pb_miccg(): CG l_maxitn exceeded!
> Total surface charge NaN
> Reaction field energy NaN
> Cavity solvation energy 2.3769
>
> I increased the linit from 1000 to 5000, but it didn't help.
>
> File generated by MMPBSA.py
> &cntrl
> ntb=0, cut=999.0, ntpr=1, imin=5,
> maxcyc=0, igb=10, ipb=1, inp=1,
> /
> &pb
> dbfopt=1, epsin=1, epsout=80, istrng=100.0,
> radiopt=0, sprob=1.4, space=0.5, maxitn=5000,
> cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4,
> /
>
> Any suggestions will be highly appreciated.
>
> Thanks
> Anu
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Oct 05 2010 - 17:30:05 PDT
