Dear gromacs users,
I am working a protein-ligand simulation where I would like to use amber forcefield. I have generated the protein-ligand system in charmm-gui webserver. However, I noticed that in the amber forcefield.itp file provided by the charmm-gui server does not contain any angletype for water: HW-OW-HW angle. Only the HW-OW bondtype is provided in the forcefield.itp file. Now we know that we employ SETTELES constraint algorithm to constrain the water molecules and use a rigid water model, only if we use flexible water model then we have separate bond length and angle terms in the water.itp files (e.g., tip3p.itp, tip4p.itp etc.).
My questions are:
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As there is no angletype for the HW-OW-HW angle present in the forcefield.itp file provided by the charmm-gui server, shall I include a separate angletype term for the HOH angle for water?
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We generally use rigid water models and the SETTLES constraint is defined by: 1 1 doh doo, where the first 1-is 1st atom of water molecule, the 2nd 1-refers to functiontype 1, doh and dhh refers to the distance between OW-HW and HW-HW atoms. But I don’t see any term or function that is separately constraining the HW-OW-HW bond angle to 104.5 degrees. Is that already implicit in defining the constraint for bond length? Do we not need a separate angle constraint term?
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Is it necessary to define H-O-H angletype and O-H and H-H bondtype in the forcefield.itp whenever we are using rigid water model? And what is H-H bond in water defined in forcefields?
Any help would be much appreciated, thank you.