[gmx-users] warnings about tip3

[Justin Lemkul]

On 10/6/19 4:56 AM, Ayesha Fatima wrote:
> 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.

Your topology has [settle] commented out, so the parameters are not 
correctly interpreted.

Note, however, that you cannot have multiple molecule blocks that use 
SETTLE, so everything needs to either be TIP3 or SOL; you can't use both 
simultaneously.

-Justin

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Justin A. Lemkul, Ph.D.
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