[gmx-users] (no subject)

[pooja kesari]

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