Re: [rDock-list-def] modify/use another force field for ligands

[Sergio R. C. <sru...@gm...>]

Dear Jose Manuel Gally,

As you said, Tripos 5.2 forcefield is used for the receptor.
Charmm27 and Insight parameters is only used when PSF/CRD files are
provided for the receptor. However, they are not used when the receptor is
in Mol2 format, as stated in rDock Documentation (Section 9):

MOL2 is now the preferred file format for rDock as it eliminates many of
> the atom typing issues inherent in
> preparing and loading PSF files. The use of PSF/CRD files is strongly
> discouraged. The recommendation
> is to prepare an all-atom MOL2 file with correct Tripos atom types
> assigned, and allow rDock to remove
> non-polar hydrogens on-the-fly.


The ligand forcefield is also Tripos 5.2 and can not be changed (without
modifying a lot of code).
For further information, more details about this can be found in
src/lib/RbtMdlFileSource.cxx and src/lib/RbtTriposAtomType.cxx.

Thank you!

Sergio Ruiz


2015-08-26 16:56 GMT+02:00 Jose Manuel Gally <
jos...@un...>:

> Dear rDock community,
>
> After docking molecules containing NH2 attached to aromatic ring (sp2
> nitrogen),  the two hydrogens are not in the same plane as the N-ring. I
> believe this issue came from the force field.
> I therefore analysed the force field used in rdock and noticed that
> several force fields are actually mentioned (in $RBT_HOME folder):
> - masses.rtf : Insight97and Charmm27
> - in folder sf, files Tripos52 (dihedral.prm, vdw.prm, vdw.prm.old)
>
> I think Tripos52 is applied to the receptor (correct me if I'm
> mistaken), but what for the ligand?
> How are used the parameters extracted from Charmm27 and Insight?
>
> Secondly, I would like to know if it's possible to modify/use another
> force field instead of the one implemented in rDock for ligands?
>
> Thank you for your help!
>
> Jose Manuel
>
>
>
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