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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Received on Thu Aug 09 2018 - 07:00:02 PDT
