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
Received on Tue Jun 09 2015 - 04:30:03 PDT
