Is there any step-by-step protocol/procedure for the membrane protein (bilayer) ligand Gromacs Simulation?
I could able to obtain a bilayer with the protein incorporated from the CHARMM GUI server, Now I am stuck; how to insert ligand on the system. I am looking forward to a useful site or protocol for this process onward.
Thank you so much in advance.
Hi,
usually you do docking to get the ligand coordinates. Then you use the docking pose in CGenFF to get parameters for the ligand. After that, you manually add the ligand to your system, including the parameters in topol.top
Hi both,
you cannot just include the "XXX.itp" in topol.top, you also need the "XXX.prm" file.
This is because, although compatible, the parameters are not the same and/or named differently.
#######################
So, immediately after the forcefield topology you add the .prm file:
; Include forcefield parameters
#include "charmm36.ff/forcefield.itp"
#include "XXX.prm"
########################
Then, you include the topology after the protein (or membrane) after the last dihedral line (or position restraint):
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include small molecule topology
#include "XXX.itp"
; Include water topology
#include "charmm36.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "charmm36.ff/ions.itp"
[ system ]
; Name
Protein with XXX in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
XXX 1
SOL 11639
CL 5
Hope it helps!
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