Re: [AMBER] PrmtopError: Inconsistent charge definition for atom

From: Jason Swails <jason.swails.gmail.com> Date: Tue, 14 Aug 2018 22:27:45 -0400

--
Jason M. Swails 
> On Aug 9, 2018, at 9:40 AM, Santanu Santra <santop420.gmail.com> wrote:
> 
> Dear all,
> 
>          I have created four different prmtop files using xleap for the
> mm-pbsa calculation and generated a few ns production run of
> receptor-ligand solvated system. The ligand parameter was generated using
> antechamber in amber12 package.
> 
> My input file for mm-pbsa.in (as available in tutorial) ::::
> 
> 
> ==================================================
> 
> Input file for running PB and GB
> &general
>   endframe=50, verbose=1,
> #   entropy=1,
> /
> &gb
>  igb=2, saltcon=0.100
> /
> &pb
>  istrng=0.100,
> /
> 
> =========================================================
> 
> while calculating I put comppand as similar as given::
> /home/xxxxx/amber/amber12/bin/MMPBSA.py -O -i mmpbsa.in -o
> final_result_mmpbsa.dat -sp complex_solvated.prmtop -cp
> complex_vacuum.prmtop -rp receptor_vacuum.prmtop -lp ligand_vacuum.prmtop
> -y *.mdcrd
> 
> =========================================================
> I got the following error:
> 
> Loading and checking parameter files for compatibility...
> PrmtopError: Inconsistent charge definition for atom 170!
> Exiting. All files have been retained.
> =========================================================
> So I checked my pdb files and found this atom belongs to ligand.
> =========================================================
> Note: I have generated ligand_vacuum.prmtop from the mol2 file as obtained
> from antechamber and rest prmtop files by loading corresponding pdb files
> (all in xleap)
> ============================================================
> Any suggestion regarding how to overcome that error is highly appreciated.
> ============================================================
> Thanks in advance.
> 
> 
> 
> 
> 
> -- 
> Santanu Santra
> Research Scholar
> Molecular Simulation Laboratory
> Department of Chemistry
> NIT ROURKELA
> ROURKELA, 769008
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