Hi Jason,
Thanks for your reply.
The binding active site includes ATP, two Magnesium ions and a number of crystal waters. I think these waters may influence the interaction among ATP, Magnesium and surrounding amino-acid residues. So I want to know the binding energy change whether these waters are included as a part of receptor. In calculation, I want to use explicit solvent model for these waters.
The error message is "CalcError: /home/duanbg/software/amber11/bin/sander.APBS failed with prmtop com.prmtop!" And the error message occurred in _MMPBSA_complex_pb.mdout.0 file which is attatched is :
Error: A residue defined as a "fast 3-point water"
is not defined by a triangle of three bonds.
Residue 920 contains 2 bonds.
The input file for MMPBSA calculation is:
&general
startframe=1, endframe=25, interval=1,
keep_files=2,search_path=1,verbose=1,
/
&pb
istrng=0.1,sander_apbs=1,radiopt=0
/
The MD trajectory is come from NAMD 2.9 software which can be converted to *.crd format by Catdcd program. The *.prmtop files for CHARMM force field are generated by Chamber program which converting *.psf files generated by VMD software. And the command for binding energy calculation is:
mpirun -np $nprocs MMPBSA.py.MPI -O -i mmpbsa.in \
-cp ./com.prmtop \
-rp ./rec.prmtop \
-lp ./lig.prmtop \
-y ./md_6_20frame_cryw.mdcrd > mmpbsa.out
Thank you for your help!
Best wishes
Duan Baogen
From: Jason Swails
Date: 2013-04-12 14:07
To: dbaogen; AMBER Mailing List
Subject: Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
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 Fri Apr 12 2013 - 03:30:02 PDT
