Hi all, a new GROMACS user here. I am using CHARM36 for protein/ligand complex. The ligand has a chlorine atom and CGenFF adds LPH atom and the following line in the topology file:
LONEPAIR COLI LP1 CL C1 DIST 1.6400 SCAL 0.0.
Salvation and adding ions goes through. When I am trying to do complex structure energy minimization, I get the following warning:
WARNING 1 [file em.mdp]:
The largest distance between excluded atoms is 1.398 nm, which is larger
than the cut-off distance. This will lead to missing long-range
corrections in the forces and energies. If you expect that minimization
will bring such distances within the cut-off, you can ignore this warning.
I assume the problem is the lone pair. How do I solve this problem? Can I increase rcoulomb?
The minimization mdp file is below:
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; long range electrostatic cut-off
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
DispCorr = no