[gmx-users] warnings about tip3

[Ayesha Fatima]

Dear All,
I m simulating cholesterol membrane with protein embedded in water portion
of the upper leaflet of the membrane. I am using Gromacs 2019 built on
Windows 10 WSL.
My intention is to pull the protein through the membrane from one end to
the other into the water part. The membrane was built on CHARMM-GUI and it
added the TIP3 water molecules on both sides of the membrane. Using
Charmm36 in Gromacs, i prepared the protein without error.
I was able to add ions and solvate the system without any issue. Now when I
want to minimise it , i am getting warnings when running the grompp to
generate the tpr that I would like to understand.
I looked on the internet and as per advice looked the TIP3.itp. the warning
is:
WARNING 1 [file TIP3.itp, line 25]:
  Too few parameters on line (source file
  /mnt/e/gromacs/gromacs-2019/src/gromacs/gmxpreprocess/toppush.cpp, line
  1326)
And line 25 is
;[ settles ]
; i j funct length
1 1 9.572000e-02 1.513900e-01
Also the note below says
NOTE 2 [file topol.top, line 1394]:
In moleculetype 'TIP3' 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.
I checked line mentioned . given in red
[ molecules ]
; Compound        #mols
Protein_chain_a     1
CHL1            256
TIP3           7171
SOL             67764
CL               1

Any idea how to correct the error? should i have changed the TIP3 to SOL
before solvating.
thank you