On Wed, Apr 10, 2013 at 11:37 PM, dbaogen <dbaogen.gmail.com> wrote:
> 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!
>
Why are there waters in your complex files? Are they structurally
important? Are you using a structural water? What is the full context of
the error message?
We need all details of what you did with MMPBSA.py to help here.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 11 2013 - 23:30:03 PDT
