Concerning your questions, there are two issue when creating a model for
which you will run an MD simulation upon. As you noted, you have been
careful concerning the development of partial atomic charges for your
ligand. This is the first issue and is an attempt to correctly capture the
Coulomb forces. The second is concerning the force-field parameters that
govern all other forces that are present in your model, such as van der
Waals, bonds, angles, and torsions. These forces are defined by your
force-field parameters (e.g. Glycam06, parm12SB, gaff). As a complete set
of forces, your Coulomb forces need to be balanced with the other
forces-field parameters - meaning that the the partial atomic charge
methodology that was used to develop the residue/ligands was also used in
developing the force fields that you will apply. Different force fields
have used different methodologies for determining partial atomic charge
(i.e. Glycam06 charges are different than parm12SB).
When creating your leap input file, you can source different force fields.
If you source two force fields, then the parameters in the second
referenced force field will over write those of the first referenced if
they are present if both force fields. Because of this, different force
fields are generated such that the atom type names prevents this from
occurring as much as possible. Thus, parm12SB uses XX naming for an atom
type, gaff uses xx, Glycam-06j uses xX, or custom made force fields
introduce new atom types (e.g. CT in parm12SB versus CG in early versions
of Glycam-06, both describing sp3 hybridized carbons). All residues within
the Glycam-06j database will have their atoms following its naming
convention, while all parm12SB residues will follow its own naming
convention.
Now back to your question. If you have correctly named the atom types
within your ligand to follow the naming convention of the Glycam force
field that you will use, then yes you should source both. If you are
following a different atom type naming convention for your ligand, then I
would consider this to be nonstandard and would not feel comfortable giving
you an answer. It is nonstandard because you are using Glycam06 charge
development methodology with atom types (and thus parameters) that belong
to a different force field. If you used the R.E.D. server, then follow what
Francois has told you as he is the expert concerning R.E.D. and its usage.
If you are still confused by this, then take a look at the AmberTools
manual and take a look at the Glycam06 and parm94 papers. Parm94 is the
predecessor of the ParmXX force-field family, and they all use the same
basic charge development method (i.e. 2-stage resp).
Bests regards,
Karl
On Mon, Feb 24, 2014 at 2:08 PM, Arun Kumar Somavarapu <arunks.imtech.res.in
> wrote:
>
>
> Thank you Sir.
>
> I am in little bit confuse, i have ligand bound to protein whose charge
> is defined through Glycam ff, now do i have to source GLYCAM_06 ff also
> along with ff12SB.
>
> Regards
>
> On 2014-02-24 18:20, David A Case wrote:
>
> > On Mon, Feb 24, 2014, Karl Kirschner wrote:
> >
> >> If you have a pure oligosaccharides that is composed of residue found
> within Glycam04 and does not contain any unusual linkages to the protein
> (e.g. it is a nonbonded complex), then you should use the Glycam parameter
> set for the carbohydrates and the ff99SB for the protein.
> >
> > Just a minor update: we recommend using the ff12SB force field for the
> > protein. This is also compatible with Glycam, but has improved torsion
> > parameters for the protein part, and generally should give better
> results.
> >
> > ....dac
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber [1]
>
> --
> Arun Kumar Somavarapu
> Project Fellow,
> Dr. Pawan Gupta Lab,
> Protein Science and Engineering Dept,
> Institute of Microbial Tecnology,
> Sec 39-A, Chandigarh - 160036.
>
>
> Links:
> ------
> [1] http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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Received on Mon Feb 24 2014 - 07:00:02 PST
