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
>>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Jun 09 2015 - 16:00:03 PDT
