Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide

From: Lachele Foley <>
Date: Mon, 8 Jun 2015 14:42:19 -0400

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

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.)

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

============ end levan.leapin ==============

To run, use "tleap -f levan.leapin".

On Mon, Jun 8, 2015 at 10:26 AM, Surasak Chunsrivirot
<> 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

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Mon Jun 08 2015 - 12:00:03 PDT
Custom Search