Hi Lachele,
1. I am confused after reading this paper -- Molecular dynamics studies of
native and substituted cyclodextrins in different media: 1. Charge
derivation and force field performances --, which compared the performance
of GLYCAM04 and GLYCAM06 on cyclodextrins.
2. I do want to a minimization with the force field and then compare it with
QM optimized structure. But I have some difficulty in building topology
file.
Something like:
.......
SM 1.7210 0.2104 OPLS
......
appears to the end of Glycam_06g.dat. Are these vdw parameters for sulfur
atom in something like a -CH2-S-CH2- environment?
No residue as "SME" is defined in prep file, so I have to construct a
monosaccharide like { OME 0hA } first, and then change the O atom in OME to
S, and SM atom type?
Then what atomic charges should be assigned to the CG and SM atoms in 'SME'?
Should the anomeric carbon CG have a different atomic charge as well?
3. For the N -CG-CG-SM sequence, the N should correspond to an amide
nitrogen attached to C2?
Thanks for the reply.
Yun
On Thu, Sep 15, 2011 at 8:32 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Thu Sep 15 2011 - 10:30:02 PDT
