[gmx-users] RB dihedral type in amber99sb-ildn ffbonded.itp

tarak karmakar tarak20489 at gmail.com
Sat Jul 11 08:21:10 CEST 2015

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

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.

There are clues from old posts,
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
     C1'  C2'  C3'  O3'     3    0.65084  1.95253  0.00000 -2.60338 0.00000
     C1'  C2'  C3'  H3'     3    0.65084  1.95253  0.00000 -2.60338 0.00000
     C1'  C2'  O2'  HO2   3    1.71544  0.96232  0.00000 -2.67776 0.00000
In this case, I have deleted the dihedral parameters in the ffbonded.itp

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

Would you like to suggest me something related to this?


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