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
>> >> > _______________________________________________
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>> >> > AMBER.ambermd.org
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>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> :-) Lachele
>> >> Lachele Foley
>> >> CCRC/UGA
>> >> Athens, GA USA
>> >>
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>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 15 2011 - 12:00:03 PDT
