[gmx-users] How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??

Vishwambhar Bhandare vishwayogi at gmail.com
Mon Mar 12 10:11:05 CET 2018


Dear users,

I want to perform implicit simulation for a protein-ligand complex.
for a protein alone, implicit works fine, but for ligand atoms it shows
error as copied below,

Setting gen_seed to -1914387900
Velocities were taken from a Maxwell distribution at 300 K
GB parameter(s) missing or negative for atom type 'N3'
GB parameter(s) missing or negative for atom type 'H'
GB parameter(s) missing or negative for atom type 'CT'
GB parameter(s) missing or negative for atom type 'HP'
GB parameter(s) missing or negative for atom type 'HC'
GB parameter(s) missing or negative for atom type 'H1'
GB parameter(s) missing or negative for atom type 'S'
GB parameter(s) missing or negative for atom type 'C'
GB parameter(s) missing or negative for atom type 'O'
GB parameter(s) missing or negative for atom type 'OH'
GB parameter(s) missing or negative for atom type 'HO'
GB parameter(s) missing or negative for atom type 'H5'
GB parameter(s) missing or negative for atom type 'H4'
GB parameter(s) missing or negative for atom type 'HA'
GB parameter(s) missing or negative for atom type 'MG'
GB parameter(s) missing or negative for atom type 'P'
GB parameter(s) missing or negative for atom type 'OS'
GB parameter(s) missing or negative for atom type 'H2'
GB parameter(s) missing or negative for atom type 'c1'

Program: gmx grompp, version 2016.4

Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1296)
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 19 atomtypes or they might be negative.


How can I get the parameters defined in gbsa.itp file..???


-- 
Dr. Vishwambhar Vishnu Bhandare
Post Doctoral Fellow
Department of Biosciences and Bioengineering
Indian Institute of Technology
Bombay-400076


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