GROMACS version: 2018.8
Hi, everyone!
I am working on a protein-ligand complex system, I wanna save 2 water molecules in the ligand binding pocket and apply position restraint for O atom. According to some discussion online, firstly I use pdb2gmx to prepare the protein and crystal water’s topology file (named 4oa4_processed.gro), then I copy the ‘tip3p.itp’ file and give the file a new name ‘tip3p1.tip’ , fill in a new name ‘FIX’ for the [ molecule_type ] in this .itp file, and also delete the [ settles ] section. Then, I include the tip3p1.tip and ligand .itp file in my .top file and change the ‘SOL’ to ‘FIX’. Details are showed in the attached .top file. When I use grompp to add ions, notes occurs as follows:
‘’
NOTE 3 [file topol.top, line 45825]:
In moleculetype ‘FIX’ 3 atoms are not bound by a potential or constraint
to any other atom in the same moleculetype. Although technically this
might not cause issues in a simulation, this often means that the user
forgot to add a bond/potential/constraint or put multiple molecules in
the same moleculetype definition by mistake. Run with -v to get
information for each atom.
‘’
It seems that it failed to add restraint to FIX, namely the crystal water. I don’t know how to solve it.
----------------------------------------------------the .top file-------------------------------------------
; Include Position restraint file
#ifdef POSRES
#include “posre.itp”
#endif
; Include ligand topology
#include “sin.itp”
; Include fixed water topology
#include “./charmm36-feb2021.ff/tip3p1.itp”
#ifdef POSRES
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include water topology
#include “./charmm36-feb2021.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-feb2021.ff/ions.itp”
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
sin 1
FIX 2
SOL 18462
--------------------------------------the tip3p1.tip------------------------------------------------------
[ moleculetype ]
; molname nrexcl
FIX 2
[ atoms ]
; id at type res nr residu name at name cg nr charge
#ifdef _FF_CHARMM
1 OT 1 FIX OW 1 -0.834
2 HT 1 FIX HW1 1 0.417
3 HT 1 FIX HW2 1 0.417
#endif
#ifdef FLEXIBLE
#ifdef ORIGINAL_TIP3P
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 502416.0 0.09572 502416.0
1 3 1 0.09572 502416.0 0.09572 502416.0
[ angles ]
; i j k funct angle force.c.
2 1 3 1 104.52 628.02 104.52 628.02
#else
;CHARMM TIP3p
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 376560.0 0.09572 376560.0
1 3 1 0.09572 376560.0 0.09572 376560.0
[ angles ]
; i j k funct angle force.c.
2 1 3 1 104.52 460.24 104.52 460.24
#endif
#else
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
The second question is that how to apply position restraint for FIX’s O atom during NVT/NPT equilibrium phase. I think I need to use ‘define = -DPOSRES’ and ‘tc-grps = Protein_sin_FIX Water_and_ions’, the ‘Protein_sin_FIX’ stands for the group made by protein, ligand and crystal water. And when running run production MD, I need to release the restraints by not using ‘define = -DPOSRES’ and using ‘tc-grps = Protein_sin_FIX Water_and_ions’. Is it right?
This problem has bothered me for one week. Any suggestion would be of great help to me. Thanks a lot!
Followed Mr. Jalemkul's advice in this post [https://gromacs.bioexcel.eu/t/solvent-partition/1034](https://gromacs.bioexcel.eu/t/solvent-partition/1034), after deleting the [ settles ] section, I use a [ constraints ] block as follows, then the Note above disappeared.
[ constraints ]
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139