Hello Sir,
Mine is a docked complex, the ligand is bonded through H-bonds.
i have generated charges for ligand by Glycam ff.
while generating topology files for complex, i used
source leaprc.GLYCAM_04
source leaprc.gaff
source leaprc.ff99SB
and generated topology files successfully.
is it right way to perform. is it considering Glycam ff here?
On 2014-02-24 15:27, Karl Kirschner wrote:
> 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. _______________________________________________ AMBER mailing list AMBER.ambermd.org 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 - 02:30:02 PST
