On Tue, 2014-08-26 at 00:36 +0800, Dhananjay wrote:
> I am relatively new to MMPBSA calculations and trying to run mmpbsa for
> protein-protein interactions with 'multiple trajectory protocol'.
>
> I have MD trajectories for complex, ligand and receptor.
> Before MD run, I make sure that the # of atoms(complex.pdb) = # of
> atoms(receptor.pdb+ligand.pdb).
>
> I used following command to run mmpbsa:
>
> mpirun -np 8 MMPBSA.py.MPI -O -i mmpbsa.in -cp
> ../preparation/complex-vac1.prmtop -sp complex-bondi.prmtop -rp
> rec-bondi.top -lp lig-bondi.top -srp receptor-bondi.prmtop -slp
> ligand-bondi.prmtop -y
> ../mult_traj_prot/complex/04_MD_run/protein_prod_nvt.mdcrd -yr
> ../mult_traj_prot/receptor/04_MD_run/protein_prod_nvt.mdcrd -yl
> ../mult_traj_prot/ligand/04_MD_run/protein_prod_nvt.mdcrd
[snip]
>
> Although, I am getting "MM/PBSA processing is done !" ther are still "-nan"
> values in the output.
> How can I fix this problem ?
> Is my protein-protein complex system is too large ?
> OR I missed something here ?
These problems almost always indicate an incompatibility between the
generated trajectory files and the prmtop files you fed to MMPBSA.py.
Visualize the trajectories that were generated
(_MMPBSA_receptor.mdcrd.0, _MMPBSA_ligand.mdcrd.0, ...etc) with the
corresponding prmtop files (rec-bondi.top, lig-bondi.top, etc.) My bet
is that the structures look completely messed up.
Oftentimes, this is caused because the default strip_mask either strips
out too many items (if you have a metal ion or water bound somewhere,
for instance), or it is not stripping enough stuff.
The default value of strip_mask is shown in the Amber 14 manual in the
MMPBSA.py chapter.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Aug 25 2014 - 10:30:02 PDT
