Thank you very much Karl for a detailed explanation, now i understand
the point.
In my case i have generated ligand charges from Red Dev server by using
Glycam_04 ff and i have not changed any atom types which leads to
nonstranded, like i mentioned earlier i sourced Glycam_06 ff, Gaff and
ff99SB ff respectively for building complex.
In Amber12 I came across leaprc.GLYCAM_06h-12SB ff, would it be useful
in my case which can cover both glycam and 12SB parameters?
Regards
On 2014-02-24 20:20, Karl Kirschner wrote:
> 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] [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 [1]
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--
Arun Kumar Somavarapu
Project Fellow,
Dr. Pawan Gupta Lab,
Protein Science and Engineering Dept,
Institute of Microbial Tecnology,
Sec 39-A, Chandigarh - 160036.
Links:
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Received on Mon Feb 24 2014 - 09:00:07 PST
