I am currently trying to replicate the Kinase resistance mutation work from Bert DeGroot lab using PMX . I am facing a bunch of errors in generating PMX gro files for the protein ligand system. I am following the following protocol:
I tried to generate the hybrid topology of the protein through the PMX Webserver and I have the cgenff parameters for the small molecule. However when i try combine hybrid protein and small molecule topologies and subsequently solvate and ionize the get the following errors
"ERROR 1 [file hybrid.itp, line 3]
No such combination rule 32759
I have tried to modify hybrid.top in the following ways:
#include “charmm36mut.ff/forcefield.itp”
#include “hybrid.itp”
#include “sti.prm”
#include “sti.itp”
#include “charmm36mut.ff/tips3p.itp”
#ifdef POSRES_WATER
[ position_restraints ]
1 1 1000 1000 1000
#endif
#include “charmm36mut.ff/ions.itp”
[ system ]
PMX MODEL in water
[ molecules ]
Protein_chain_A 1
Finally i generate the system using the following set of commands
gmx editconf -f complex.pdb -o box.pdb -bt dodecahedron -d 1.0
#and we fill it with water:
gmx solvate -cp box -cs spc216 -o water.pdb -p hybrid.top
#To prepare the first energy minimization download the em.mdp file and run:
gmx grompp -f em.mdp -c water.pdb -p hybrid.top
Is there a way to process the small molecule topology so that the atom types can be read from the hybrid charmm/cgenff topology or from the orignal charmm/cgenff toplogy.
Regards
Mrinal