Dear All, I am doing a protein-ligand simulation, when i was try to *add ions to the system* gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr *there was an error* Fatal error: Syntax error - File lig.prm, line 2 Last line read: '[ bondtypes ]' Invalid order for directive bondtypes *my topol.top- ligand defination is as follows * ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif
; Include ligand parameters #include "lig.prm" ; Include ligand topology #include "lig.itp" ; Include water topology #include "./charmm36-mar2019.ff/tip3p.itp" I have included the ligand parameter details as suggested in lig.top file generated by cgenff python script. I have attached the itp and prm file for reference. Thanks & Regards, Dr. Pooja Kesari Post Doctoral Fellow Department Of Biosciences and Bioengineering Indian Institute of Technology Bombay INDIA
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