Dear all,
I want to calculate binding free energy including crystal water using MMPBSA.py in Amber 11 with AmberTools 12 under CHARMM 27 FF. The CHARMM FF parameters are converted by Chamber program in Amber using the following command:
chamber -top top_all27_prot_lipid_na.inp -param par_all27_prot_na.inp -psf ${str}_charmm.psf -cmap -tip3_flex -crd ${str}.pdb -p ${str}.prmtop -inpcrd ${str}.inpcrd -verbose
But in calculation, the MMPBSA.py script gives the error message " Error: A residue defined as a "fast 3-point water is not defined by a triangle of three bonds. Residue 920 contains 2 bonds." Does it mean that the angle parameter for H-O-H is not found?
And what should I do to fix this problem? Would you like give me some help? Thanks!
Best wishes
Duan Baogen
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Received on Wed Apr 10 2013 - 21:00:02 PDT
