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

[Justin Lemkul]

On 7/11/15 2:21 AM, tarak karmakar wrote:
> 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

Don't use distance restraints.  Use the pull code.  That's what it is for.

> 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
>

Merging this information should not be necessary.  Simply adding the new 
parameters in the ligand's .itp file should take care of everything, provided it 
is #included in the proper sequence.

-Justin

> 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,
> 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?
>
> Thanks,
> Tarak
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================