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From PDB to GROMACS via OPLS

If you are here is because you want to simuate some molecule with GROMACS using the OPLS force field...

Getting the force field files

  • The first thing we need is a PDB file of your molecule. For the sake of clarity, let's assume that the name of the molecules is "molecule" and thatn the residue is RES
  • Then you plug it into TPPMKTOP . You can read their manual on how to use the program
  • You will then get two results:

.rtp file and .itp file

  • The first conatins the residue type and the second the description of the molecule.

 Now let's add this into GROMACS opls force field

  • Search for the oplsaa.ff in your computer to know where your force fields are in your computer. The folder should be called something like  gromacs-2018/share/top.
  • Open the file residuetypes.dat in the top folder and add the name. Even more specific write inyour file something like

RES  solvent

  • The word "solvent" is not important. This is done so that this residue exists for GROMACS
  • Open now the folder opls.ff
  • Copy the itp file from TPPMKTOP in your folder
  • Open forcefield.itp and add your itp by taping

#include "molecule.itp"

  • Finally, open the .rtp file from the opls force field in opls.ff and copy the .rtp file from TPP at the end of the .rtp file (in my case it is aminoacids.rtp)

Generating the top file

  • Now you have included your molecule in the force field opls you can generate the files necessary to do a simulation. To do that use pdb2gmx program

 

 

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