[gmx-users] Running MD simulation with Multiple ligands

Chamikara Herath chamikara.herath at sjp.ac.lk
Thu Oct 26 08:08:55 CEST 2017

I need to run a MD simulation with two ligands

01. Natural Substrate (GTP)
02. Allosteric drug candidate bounds closer to the substrate binding pocket.

single itp file was created , combining both ligands using Swiss pharm for
CHARMM force field.

I am unable to continue from the add ion step because the following error
message always happens when grompp is tried to run

*Fatal error:Syntax error - File gtp_bergenin.itp, line 7Last line read:'[
atomtypes ] 'Invalid order for directive atomtypes*
I am following the following tutorial
GROMACS TutorialProtein-Ligand Complex

*Justin Lemkul*
*Department of Biochemistry, Virginia Tech*

*please kindly advice me on come across this error. *

*I can provide topology files *

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