Hi there,
1.
In the end of this file, it notes that ".....in conjunction with Parm94
without introducing any conflict.....". So what about in combination with
parm99 force field parameter set, would there be any foreseeable problems?
It seems many people are still using Glycam_04 series parameter set for
carbohydrate. I wonder if GLYCAM06 parameter sets are not as good as
GLYCAM04 in terms of simulating pure carbohydrates?
2.
In Glycam_06_alldocs.txt, it says that for Glycam_06g.dat, "Changes include
adding a comprehensive thiol-linkage set for glycosidic linkages formed by a
Sulfur". So I looked into it, and found some differences between the ideal
bond and angle values in the data set and those calculated for a sample
molecule from QM.
I constructed a Met-S-alpha-L-Rhamose molecule, then did three QM geometry
optimizations using HF 6-31G*, starting from three different conformations.
All three optimized structure showed a CG-SM bond length of about 1.83
angstrom, while the value is 1.81 angstrom in Glycam_06g.dat. And most
angles involved in the thiol-glycosidic linkage are off the values in
Glycam_06g.dat by 1 to 10 degrees.
I understand angle parameters for i.e. CG-SM-CG are taken from cysteine. So
I wonder if it's reasonable to still go head with what are Glycam_06g.dat if
I am simulating a ligand containing this -S-alpha-L-Rham- part?
3.
I also found something like:
NH-CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0
SCNB=1.0 Thiol-linkages
in Glycam_06g.dat. Is this 'NH' a typo? If it is, what kind of nitrogen atom
is it referring to? Like the nitrogen attached to C2 in a carbohydrate
derivative?
Thanks for any advice.
Regards,
Yun
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Received on Wed Sep 14 2011 - 16:00:02 PDT
