Hi Matthew,
That's almost exactly what I planed to do!
Thanks,
Yun
On Thu, Sep 15, 2011 at 11:53 AM, Matthew Tessier <matthew.tessier.gmail.com
> wrote:
> Yun,
> I developed part of the thiol-linkage parameter sets and a former graduate
> student developed the initial parameter sets. We had planned to use them
> on
> some synthetic glycans but that project didn't get funding. The
> thiol-linkage parameters should be carefully employed and stringently
> validated against experimental data since they were only developed on QM
> models.
>
> I don't plan on developing new prep files for thiol-linkage glycans
> however,
> there is no reason you can't take the existing prep files and replace the
> linkage atom type "OS" and replace that with "SM". The only thing you'll
> have to do is re-develop charges which can be done with the RED server if
> you'd like. Be sure to generate Ensemble Averaged charges for each residue
> that you use.
>
> Please let me know if you have any additional questions.
>
>
> Matthew B. Tessier
> Complex Carbohydrate Research Center
> University of Georgia
> +1 (706) 542-3508
> mbt3911.uga.edu
> matthew.tessier.gmail.com
>
>
>
> -----Original Message-----
> From: Lachele Foley (Lists) [mailto:lf.list.gmail.com]
> Sent: Thursday, September 15, 2011 2:40 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
>
> We'll take a look at the paper.
>
> I can't make any promises about the prep file, but I'll see if anyone
> has something in an advanced stage.
>
>
> On Thu, Sep 15, 2011 at 2:07 PM, Yun Shi <yunshi09.gmail.com> wrote:
> > 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
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> :-) Lachele
> >> >> Lachele Foley
> >> >> CCRC/UGA
> >> >> Athens, GA USA
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 15 2011 - 16:00:02 PDT
