GROMACS modification: /No
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I have two ligands, ligand1 is the acid form of a buffer with 0 charge, ligand2 is the basic form of a buffer with -1 charge. Two ligands are mostly identical except ligand2 does not have a hydrogen so it is -1 charged. I submit their PDB to acpype and got ligand1.gro/top/itp and ligand2.gro/top/itp files.
insert-molecules and update the topol.top files based on here. If only one ligand is inserted, there is no problem to run
gmx grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr -maxwarn 1
But if both ligands are inserted, the
gmx grompp -f ions.mdp ... will give error:
Fatal error: Syntax error - File ligand2.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes
I have already put the itp lines in the very beginning of the
; Include forcefield parameters #include "amber14sb.ff/forcefield.itp" #include "ligand1.itp" #include "ligand2.itp"