I corrected the NH issue. We've also implemented some versioning
that should be helpful.
See glycam.org/params
Let me know if you have trouble.
On Thu, Sep 15, 2011 at 2:39 PM, Lachele Foley (Lists)
<lf.list.gmail.com> wrote:
> 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
>>> >>
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>>>
>>>
>>>
>>> --
>>> :-) Lachele
>>> Lachele Foley
>>> CCRC/UGA
>>> Athens, GA USA
>>>
>>> _______________________________________________
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 15 2011 - 14:00:02 PDT
