Dear All,

I need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use the ligand.itp externally, I can not impose the distance restraints between the protein and the ligand. Then, I tried to include (merge) the parameters of the ligand to specific files present in the amber99sb-ildn directory.

I tried the following,

atomtypes.atp => atomtypes (gaff) of the ligand molecule are appended.

aminoacids.rtp => generated a new .rtp entry for the ligand molecule,

ffnonbonded.itp => non-bonded parameters are appended

ffbonded.itp => copied and pasted the bond, angle parameters, and RB dihedrals

Now, the problem I am facing with the dihedral, the implementations of RB type (type 3) and proper dihedral type 9.

It seems pdb2gmx does not read the dihedrals specified in the ffbonded.itp for the ligand molecule.

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There are clues from old posts,

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097280.html

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-April/080306.html

Include the dihedral parameters after the [ bonds ] section in the .rtp file like,

[ dihedrals ]

C1' C2' C3' C4' 3 3.68192 3.09616 -2.09200 -3.01248 0.00000 0.00000

C1' C2' C3' O3' 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000

C1' C2' C3' H3' 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000

C1' C2' O2' HO2 3 1.71544 0.96232 0.00000 -2.67776 0.00000 0.00000

....

In this case, I have deleted the dihedral parameters in the ffbonded.itp file.

However, it does not seem to solve the problem. :(

Would you like to suggest me something related to this?

I have the same posted the same question in gromacs mailing list.

Thanks,

Tarak