Lachele,
Thank you very much for your prompt response and clear explanation. I
really appreciate it.
I understand the charge adjustment for this branched levan now.
Regards,
Surasak
On Wed, Jun 10, 2015 at 5:35 AM, Lachele Foley <lf.list.gmail.com> wrote:
> Thank you for the question. I have updated the documentation to be
> clearer.
>
> These are the updates I made:
>
> 1. Added a brief definition of formal charge within the context of the
> instructions.
>
> 2. Clarified the instructions to emphasize their dependence on the
> possession of a residue pre-configured for the proper branching. I
> also added brief information for handling exceptions (that is,
> residues where a hydroxyl H must be removed).
>
> Here are explanations of the updates as applied to your situation:
>
> 1. Regarding the term 'formal charge': Here, I am referring to the
> number of extra or missing electrons that the derivative will bring to
> the final molecule. For example, a sulfate group (SO3-) brings a
> charge of -1 and an NH3+ group brings +1. Since you are adding
> neutral sugar residues, the formal charge is zero.
>
> 2. Your branching pattern does not already exist in the prep database
> (this is why you needed to remove the hydrogen). You first need to
> adjust the charge at the oxygen to maintain the modularity described
> at the top of the page. Since each branch point must carry -0.194 of
> the charge across a linkage, the oxygen must absorb the difference
> between that and the charge left over when the hydrogen leaves. Since
> the H has a partial charge of 0.4010, it will leave a partial charge
> of -0.4010 on the residue, which is too large. To reduce that to
> -0.194, you then add 0.207 to the charge on that oxygen.
>
>
>
> On Tue, Jun 9, 2015 at 7:05 AM, Surasak Chunsrivirot
> <chunsrivirot.gmail.com> wrote:
> > Hi Lachele,
> >
> > Thank you very much for your help. I really appreciate it. I used your
> > script to build the branched levan, and it works perfectly.
> >
> > I have another question regarding the charge adjustment at main3.O1.
> > Originally, it was -0.624 and you changed it to -0.4170 (set main.3.O1
> > charge -0.4170). The factor of 0.207 was added to the original charge of
> > -0.624. I have already read the charge adjustment procedure from (
> >
> http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
> ).
> > In my case, the branched group (6CU 0CU) has the following values:
> > fCh = 0.401 (from the charge of main.3.H1O that was deleted)
> > rCh = 0.194 (from the total charge of 6CU 0CU)
> > dCh = fCh - rCh = 0.401-0.194 = 0.207
> > iCh = 0 ?
> > dCh - iCh = 0.207-0 = 0.207 --> The factor that was added to the original
> > charge of -0.624 of main.3.O1.
> >
> > Do I understand this correctly? I'm wondering why iCh = 0 in this case.
> >
> > Thank you very much for your help,
> > Surasak
> >
> >
> >
> >
> > On Tue, Jun 9, 2015 at 1:42 AM, Lachele Foley <lf.list.gmail.com> wrote:
> >
> >> Sorry I was slow responding to your other email. This is a better
> >> forum in any case. Others might have similar questions.
> >>
> >> There is no name for that residue. But, you don't technically need
> >> one if you are willing to learn to use tleap (or xleap if you prefer).
> >> The "easy" residues that are in the manual were made to cover the most
> >> commonly studied mammalian glycans. We couldn't make up names for
> >> everything. It isn't possible to cover everything in three
> >> characters.
> >>
> >> Your image also shows an anomeric-to-anomeric termination with DGlcpa.
> >> I'm including that in this explanation.
> >>
> >> In the file copied below, I change the charge on an oxygen. The
> >> following is a link to documentation explaining a little about how to
> >> determine the proper charge. The info is for a different sort of
> >> system, but similar logic applies. (In this situation, you can also
> >> learn the prep file well enough to guess the charge from other
> >> residues, but I won't explain that.)
> >>
> >>
> http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
> >>
> >> Here is a tleap input file that will build what you want. See the
> >> comments for explanations for each step. The structure made with this
> >> still needs minimizing.
> >>
> >> Please check the resulting structure carefully to be sure I understood
> >> you and read the image properly.
> >>
> >> =========== begin levan.leapin ==============
> >> # load the glycam params
> >> source leaprc.GLYCAM_06j-1
> >>
> >> # Build the main chain, including the glucose 1-2 terminal
> >> # Note that the build goes from reducing to non-reducing
> >> main = sequence { 1GA 6CU 6CU 0CU }
> >>
> >> # remove the hydrogen at position one of the third residue
> >> remove main.3 main.3.H1O
> >>
> >> # set a new charge and type for the linking oxygen
> >> set main.3.O1 charge -0.4170
> >> set main.3.O1 type "Os"
> >>
> >> # set the tail of the sequence to that same residue
> >> set main tail main.3.O1
> >>
> >> # add the other two residues
> >> main = sequence { main 6CU 0CU }
> >>
> >> # set a dihedral at the 2->1 linkage at res 3 because of horrible clash
> >> impose main { 3 } { { "O5" "C2" "C1" "O1" -60.0 } }
> >>
> >> # have leap check the structure
> >> check main
> >>
> >> # save simulation input files
> >> saveamberparm main levan.parm7 levan.rst7
> >>
> >> quit
> >> ============ end levan.leapin ==============
> >>
> >> To run, use "tleap -f levan.leapin".
> >>
> >>
> >> On Mon, Jun 8, 2015 at 10:26 AM, Surasak Chunsrivirot
> >> <chunsrivirot.gmail.com> wrote:
> >> > Hi,
> >> >
> >> >
> >> >
> >> > I want to build a branched levan oligosaccharidge, consisting of
> >> > D-fructofuranosyl
> >> > residues predominantly linked by *β*-(2, 6) linkage in a main chain
> with
> >> a
> >> > *β*-(2, 1) linked branching point (an example structure was sent along
> >> with
> >> > this email).
> >> > I tried to find the name of residue A in AmberTools13: Reference
> manual
> >> but
> >> > I couldn’t find the name of a fructosyl residue with 1,(2),6 linkage
> like
> >> > that of residue A. I’m wondering if it is possible to build this
> branched
> >> > levan using AMBER (Glycam). If it is, would you please tell me the
> name
> >> of
> >> > this fructosyl residue A with 1,(2),6 linkage?
> >> >
> >> >
> >> >
> >> > Thank you very much for your help. I really appreciate it.
> >> >
> >> >
> >> >
> >> > Regards,
> >> >
> >> > Surasak
> >> >
> >> > _______________________________________________
> >> > 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
>
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>
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Received on Tue Jun 09 2015 - 20:00:02 PDT
