1. GLYCAM06 should be used instead of GLYCAM04. The point of
GLYCAM06 is that it does a better job. Like I said in the other
email, if you find any place where 04 is significantly better than 06,
please let us know. It should work well with other good protein force
fields. The basic idea, and there might be times when this is not so
valid, is that if you make a really good, general force field for
carbohydrates and a really good, general force field for proteins,
they should, when used in concert, do a pretty good job modeling what
proteins and carbohydrates do together.
2. Any angle or bond length observed in a molecule is the combination
of many different parameters. For example, if I build and minimize
N-acetyl neuraminate { ROH 0SA }, I find that the bond length between
the ring oxygen and the anomeric carbon is 1.44. Their atom types are
OY and CY, respectively. The parameter file, however, gives the
equilibrium bond length for those two types as being 1.410. The
difference is because all the parts of the molecule, all the different
angle, bond and torsion parameters, push and pull on each other.
Certain aspects of any structure, therefore, are expected to deviate
from the values found in the parameter file. So, you can't look at a
QM bond length or angle from within an entire molecule and expect it
to be exactly the same as any individual parameter. Conversely, you
cannot, with great precision, predict the bond lengths or angles in a
molecule based on individual values in the parameter file. If you
want to know the final values in a molecule, you have to build the
molecule and, at the very least, minimize it using the force field.
All of our parameters are taken from small molecule analogs. This is
a design philosophy that seems to work well and is generally not a
cause for concern.
3. It is, indeed, a typo. It should be:
N -CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0
SCNB=1.0 Thiol-linkages
I will get corrected versions up on our site by the end of the day.
Type "N" is defined at the top of the file.
:-) Lachele
On Wed, Sep 14, 2011 at 6:53 PM, Yun Shi <yunshi09.gmail.com> wrote:
> 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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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 15 2011 - 09:00:02 PDT
