Hi Yun,
I have solved similar problem some time ago. Here are relevant
discussions:
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex
system ?
http://archive.ambermd.org/200904/0290.html
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex
system ? - Last detail
http://archive.ambermd.org/200904/0372.html
Best,
Marek
Dne Fri, 19 Aug 2011 20:48:01 +0200 Yun Shi <yunshi09.gmail.com> napsal/-a:
> Thanks a lot Lachele.
>
> I do have other thio-glycosidic compounds with J-coupling data that I
> want
> to do MD simulation with.
>
> But before trying the dividing methods I propose, I am still wondering
> what
> are the techniques to modify parameters such as an ideal bond lengths
> and a
> dihedral force constant. Should I do this through a .frcmod file?
> Because I
> found the .prmtop so difficult to interpret, not to mention to modify.
>
> Regards,
>
> Yun
>
>
> On Fri, Aug 19, 2011 at 10:39 AM, Lachele Foley (Lists)
> <lf.list.gmail.com>wrote:
>
>> First, yes, it is possible to divide the molecule into parts and treat
>> the parts the way you describe. Since you will be doing something a
>> bit novel, you definitely need to validate the model you generate.
>> But, yes, you can do that.
>>
>> > So if I find things not in accordance with experimental data, what
>> can I
>> do
>> > to change it manually?
>>
>> That's not a simple question to answer. In part, it depends what you
>> find that isn't in accordance. Whatever you do, you need to be
>> careful. The parameters are interrelated, and what counts isn't the
>> specific value of any one parameter, but the values taken by the
>> specific bonds, angles, etc., in a minimized or simulated molecule.
>>
>> That is, if you vary one parameter, say a bond equilibrium value, to
>> be exactly what you expect it to be, you might find that you've thrown
>> other values out of whack. Once you fix those, your bond parameter
>> might be ok, but when placed in a molecule and minimized, you might
>> never observe the value you wanted.
>>
>> In relation to that, is also important to note that these force fields
>> are developed to be somewhat general. That is, any given structure is
>> likely to behave very similarly to its real counterpart within
>> contexts appropriate to the force field, but they are still
>> approximations. In other words, all the values are likely to be a
>> little bit off. But, in cases where the simulation is reasonable,
>> the extent to which they disagree should not be large enough to be
>> important.
>>
>> There is one other caution in comparing to experiment: compare to the
>> experimental observation whenever possible, not to the conclusion
>> drawn by the researcher. For example, assume you find a study where
>> j-couplings are used to determine certain torsions. The torsions
>> reported in the study are conclusions the researcher made based on
>> observed j-couplings. It is better to run a simulation and predict
>> observed j-couplings from the ensemble-averaged, simulated torsions.
>> Then, compare the j-couplings you predict to those that are observed.
>>
>> :-) L
>>
>> On Fri, Aug 19, 2011 at 12:31 PM, Yun Shi <yunshi09.gmail.com> wrote:
>> > Hi Lachele,
>> >
>> > So if I find things not in accordance with experimental data, what
>> can I
>> do
>> > to change it manually?
>> >
>> > Is it technically possible to do it due diligence in the first place?
>> That
>> > is, cut the molecule into three parts as I mentioned before, use
>> GLYCAM
>> for
>> > the sugar part, 99SB for the Thr, and GAFF for modified Phe and the
>> > thio-glycosidic linkage. And may I then link these parts together
>> using
>> LEaP
>> > ?
>> >
>> > Thanks,
>> >
>> > Yun
>> >
>> > On Tue, Aug 16, 2011 at 12:39 PM, Lachele Foley (Lists)
>> > <lf.list.gmail.com>wrote:
>> >
>> >> GAFF should get you a reasonable result. You'd definitely need to do
>> >> some validation to be sure things are working right (check angles or
>> >> H-bonding or whatever you can find experimental values for). You
>> >> might ask if it matters. For example, if you are simulating a
>> tightly
>> >> bound complex, then the glycosidics can't change anyway. If they can
>> >> change, then you need to find some way to determine whether or not
>> the
>> >> method is working. It would take significant work to get Glycam
>> >> working with all parts of this system.
>> >>
>> >>
>> >> On Tue, Aug 16, 2011 at 2:34 PM, Yun Shi <yunshi09.gmail.com> wrote:
>> >> > Hi all,
>> >> >
>> >> > I have a small molecule that consists of a Thr with an ACE cap, a
>> >> modified
>> >> > (CO becomes CH2) Phe, and a rhamnose linked to Phe via a
>> thio-glycosidic
>> >> > linkage. And please see attached the molecule I drew.
>> >> >
>> >> > While the Thr and Rha are the standard building blocks of GLYCAM06
>> and
>> >> 99SB
>> >> > force fields respectively, what about the modified Phe and the
>> >> > thio-glycosidic linkage?
>> >> >
>> >> > As what seemed to be discussed before in the archive, GAFF can be
>> applied
>> >> to
>> >> > the entire molecule. But the sugar ring is very sensitive to
>> dihedral
>> >> > parameters, right? So the GAFF parameters (and am1-bcc charges) may
>> not
>> >> be
>> >> > good enough for sugar?
>> >> >
>> >> > Thus, I wonder if it's possible to add all the bond, angle,
>> dihedral,
>> and
>> >> > charge parameters for the modified Phe and the thio-glycosidic
>> linkage
>> by
>> >> a
>> >> > .frcmod file. But where can I find proper parameters for
>> thio-glycosidic
>> >> > linkage? Could anyone tell me the steps (formats) to construct
>> such a
>> >> > .frcmod file?
>> >> >
>> >> > Any help is appreciated!
>> >> >
>> >> > Thanks,
>> >> >
>> >> > Yun Shi
>> >> >
>> >> > _______________________________________________
>> >> > 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
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>> >>
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>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
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>>
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Received on Mon Aug 22 2011 - 11:00:04 PDT
