[AMBER] MMPBSA.py problem

From: s. Bill <s_bill36.yahoo.co.uk>
Date: Sun, 14 Mar 2010 10:56:25 +0000 (GMT)

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
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