Hi Lachele,
Here is the link I used:
http://pubs.rsc.org/en/content/articlelanding/2011/cp/c1cp20854c
Should I expect a new version of prep file to include thiol glycosidic
linkage in a few weeks? If not, I will try to do it myself.
Thanks again.
Yun
On Thu, Sep 15, 2011 at 10:41 AM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> 1. Web of Science does not report finding an article containing the
> words "Molecular dynamics studies of native and substituted
> cyclodextrins in different media" in the title. Can you give a more
> complete reference?
>
> 2-3. At the top of the parameter file, you will find atomic mass
> definitions with useful comments. For example:
>
> N 14.01 sp2 N amide group
> SM 32.06 sulfane carbohydrate linkage
> (-CH2-S-CH2-)
>
> 2. Thiol linkages are still in the development phase. That's why
> information for them occurs only in parameter file releases since the
> GLYCAM06 paper. If you want to use them, you will have to generate
> your own prep file entries. To do this, you need to generate
> ensemble-averaged charges for the species you wish to model. You
> should use the procedure as discussed in the GLYCAM06 paper. You
> might be able to loosely base a prep entry on an existing one, but
> that is best done only by someone with a lot of experience doing this
> sort of modeling.
>
> :-) Lachele
>
>
> On Thu, Sep 15, 2011 at 1:03 PM, Yun Shi <yunshi09.gmail.com> wrote:
> > 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
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
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> >>
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> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Thu Sep 15 2011 - 11:30:02 PDT
