Hi,
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. The partial
atomic charges for carbohydrates and those for the amino acids were
developed using different protocols, making them only balanced with their
respective force field (e.g. aliphatic hydrorgens are treated different,
plus the force fields use different scee and scnb scaling factors, which
Amber12 supports easily). Furthermore, you should try to use the more
recent version of Glycam06.
Now if you have a ligand that is a mix between carbohydrates and amino
acids, or other nonstandard residues, then the problem becomes much more
difficult. In this case, you should develop parameters that are optimized
for use with Glycam. This can be very difficult to do and will likely
involve assigning new atom types. Once this is done then you can use your
optimized parameters with Glycam for the ligand, and the ff99SB for the
protein.
A nonideal way would be to borrow parameters from another force field
(e.g. gaff, parm99SB), convert the parameter's atom types to be compatible
with Glycam, and then verify that they reproduce some target observable
(e.g. QM torsion curves). Alternatively, you can develop partial atomic
charges that are compatible with the gaff force field, and use a
gaff/parm99SB combination and hope that it properly captures that ligand's
conformational and energetic behavior.
Best regards,
Karl
On Mon, Feb 24, 2014 at 10:12 AM, Arun Kumar Somavarapu <
arunks.imtech.res.in> wrote:
>
>
> Dear Sir
>
> I have a protein and a pseudo oligosaccharide complex. I used Red server
> and GLYCAM_04 forcefield to generate charges for oligosaccharide, now to
> generate topology files(prmtop and inpcrd) for complex can i use ff99SB
> forcefield?
>
> Thanking you.
>
> Regards
>
> --
> 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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>
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Received on Mon Feb 24 2014 - 02:00:04 PST
