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
>
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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.
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Received on Mon Feb 24 2014 - 05:30:03 PST
