How to treat specific water molecules as ligand?

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3

Hi @alevilla, thank you very much. I think I am following your instructions:

I save the default tip3p.itp as tip3p1.itp and put into my working directory, replace all the SOL strings with FIX. But I am not sure how to deal with the [ settles ] and [ exclusions ] sections. Based on this thread, I replace the [ settles ] and [ exclusions ] sections with [ constraints ], is that correct? But that thread is for “flat-bottom restraint”, what if I want to use the normal “position restraint”?


[ moleculetype ]
; molname	nrexcl
FIX		2

[ atoms ]
; id  at type     res nr  res name  at name  cg nr  charge    mass
  1   OW          1       FIX       OW       1      -0.834    16.00000
  2   HW          1       FIX       HW1      1       0.417     1.00800
  3   HW          1       FIX       HW2      1       0.417     1.00800

#ifndef FLEXIBLE
;;[ settles ]
; OW	funct	doh	dhh
;;1       1       0.09572 0.15139
;;
;;[ exclusions ]
;;1	2	3
;;2	1	3
;;3	1	2

[ constraints ]
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139

#else

[ bonds ]
; i     j       funct   length  force_constant
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_constant
2       1       3       1       104.52  628.02      104.52  628.02  

#endif

Yes, I have also updated the topology file to include the new water molecule. But I use the same POSRES for the conserved water as protein.

And yes, in the nvt.mdp and npt.mdp files, it has

define		= -DPOSRES
tc-grps		= protein_lig_conserve-water  water_ions_without-conserve-water

while in the md.mdp file, it does not have the restraints and has
tc-grps = protein_lig Water_and_ions