Swiss Institute of Bioinformatics
How to set up a GROMACS simulation with a molecule parametrized in SwissParam.Created and maintained by the Molecular modeling group, SIB.
This tutorial shows how to use SwissParam to setup a molecular dynamics simulation of a protein with a small-molecule ligand in GROMACS, using the CHARMM forcefield. When using the CHARMM forcefield in GROMACS, please cite . When using SwissParam, pleace cite .
As a particular example, we look at the protein trypsin with its aminomethylcyclohexane (AMC) ligand, as taken from the PDB entry 1TNG.
- Separate the original pdb file into two pdb files, one for the
protein and one for the small molecule.
- Open the ligand_raw.pdb file in UCSF Chimera. Choose Tools >
Structure Editing > addH.
Save as .mol2 file
ligand.mol2For alternative methods to get a .mol2 file for your ligand, see the SwissParam webpage
- Go to SwissParam and submit
the ligand.mol2 file. You will get the output in your email. Uncompress
the archive :
unzip ligand.zipFor this tutorial using GROMACS, you will only need the pdb file (with hydrogens) and the .itp file with the GROMACS topology of the ligand :
- Generate a GROMACS topology for the protein without the ligand.
This particular system includes a calcium ion. It has to be renamed in the
pdb file to match the CHARMM terminology. In the protein.pdb file,
change the calcium atom name and the residue name to CAL :
HETATM 2013 CAL CAL A 901 37.738 24.784 36.891 1.00 18.31 CAThen run the pdb2gmx program from the GROMACS suite:
pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp
- Modify the topol.top file generated by pdb2gmx. In the "Include chain topologies" section, add the
following statement, before
all other lines referring to the protein or ions :
#include "ligand.itp"This statement has to be at this precise position in the file because it contains [atomtypes] and [pairtypes] sections which have to appear in the topology before any [moleculetype] section.
Then, in the [molecules] section, right after lines indicating the number of protein and ion molecules, add the following line :
ligand 1If there are crystal water molecules in the structure, there will be a line indicating the number of solvent molecules (SOL) in the topology. In this case, the line above should be inserted before any SOL lines. See below for an example topol.top file.
- Merge the protein and ligand coordinates. Insert the ATOM lines from
the ligand.pdb into the conf.pdb file, right after the line for the ion
CAL. Atoms will be automatically renumbered in the next step.
- Now we are back to the usual GROMACS setup procedure.
editconf -f conf.pdb -o boxed.pdb -c -d 1.2 -bt octahedronIf you have an appropriate input file em.mdp for an energy minimization in GROMACS, you can then run
genbox -cs -cp boxed.pdb -o solvated.pdb -p topol.top
grompp -f em.mdp -c solvated.pdb -p topol.top
- It is possible to include position restraints on the ligand by using
the POSRES_LIGAND flag. In the case where both protein and ligand atoms
should be restrained, the corresponding line in the em.mdp file would
define = -DPOSRES -DPOSRES_LIGAND
To verify that your solvated molecule looks good in its octahedric box, you have to remember that gromacs always works
internally with an equivalent triclinic unit cell. To see the
octahedron, you will have to transform your coordinates (after having
run grompp), using :
trjconv -s topol.tpr -f solvated.pdb -o compact.pdb -ur compact -pbc mol
- It can happen that there is more that one small molecule in your
system. Due to the fact that all [atomtypes] and [pairtypes] sections
have to come before any [moleculetype] section, it is not possible to
sequentially include two or more .itp files created by SwissParam.
Instead, you will have to manually merge the contents of those itp
files, such that the right order of sections is maintained.
Example topol.top file
; Include forcefield parameters
P. Bjelkmar, P. Larsson, M. A. Cuendet, B. Hess, E. Lindahl, Implementation
of the CHARMM Force Field in GROMACS: Analysis of Protein Stability
Effects from Correction Maps, Virtual Interaction Sites, and Water
Models, J. Chem. Theory Comput., 2010, 6 (2), pp 459–466.
http://old.swissparam.ch / V. Zoete, M. A. Cuendet, A. Grosdidier, O. Michielin, SwissParam, a Fast Force Field Generation Tool For Small Organic Molecules, to be submitted