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
>>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 15 2011 - 11:00:04 PDT
