Dear AMBERI am trying to use MMPBSA.py to calculate the binding energy, where mm_pbsa.pl is not available for my system because of existence of zinc ion in my system. (I do know I can implement it in mm_pbsa_calceneent.pm file).But, the problem for mmpbsa.py is that, I have submitted my mmpbsa.in file as following
Input file:Input file for running PB and GB in parallel&general endframe=20, verbose=1, /&gb igb=2, saltcon=0.000/&pb istrng=0.000, /
It gives me an output without a calculations:|Input file for running PB and GB in parallel|&general| endframe=1, verbose=1,|/|&gb| igb=2, saltcon=0.000|/|&pb| istrng=0.000,|/|--------------------------------------------------------------|Solvated complex topology file: SolvatedComplex.prmtop|Complex topology file: Complex.prmtop|Receptor topology file: Receptor.prmtop|Ligand topology file: Ligand.prmtop|Initial mdcrd(s): Data.mdcrd||Best guess for receptor mask: ":1-292"|Best guess for ligand mask: ":293"|Ligand residue name is "X1"||Calculations performed using 1 frames.|Poisson Boltzmann calculations performed using internal PBSA solver in sander.||All units are reported in kcal/mole.--------------------------------------------------------------------------------------------------------------------------------------------------------------
I have followed the mmpbsa.py thread discussing this problem on AMBER list, so I tried using initial_traj=1 without specifying -sp prmtop file. But, it gives me the following error:Error: Sander output is missing values! BOND = ************* ANGLE = 255832.2695 DIHED = 9628.0187
How can I solve this issue?Also, I was wondering should I include the crystallic water molecules and ions in my receptor prmtop file.Thanks in advanceS. Bill
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Received on Sun Mar 14 2010 - 04:00:03 PDT
