Amber's Tutorial on Building Oligosaccharides
Tutorial
The GLYCAM website can automatically generate the following molecules and supports many additional options. The functions of the website are being expanded, and currently available functions include:
- Oligosaccharides, linear and dendritic
- Glycoprotein, linked to O or N, contains multiple sugar units
- Construct oligosaccharides by URL
AmberTools
AmberTools test file contains other examples related files are located at:
$AMBERHOME/AmberTools/test/LEaP/GLYCAM: test home directory
$AMBERHOME/AmberTools/test/LEaP/GLYCAM/06EPb: additional site oligosaccharide
$AMBERHOME/AmberTools/test/LEaP/GLYCAM/06j: main oligosaccharide directory
$AMBERHOME/AmberTools/test/LEaP/GLYCAM/06j_10: glycoprotein used in combination with ff10 force field
$AMBERHOME/AmberTools/test/LEaP/GLYCAM/06j_12SB: glycoprotein used in combination with ff12SB force field
Note
For the molecules in the test catalog, the purpose of construction is only to test AmberTools, and may not be directly used for simulation. Some conformations may be unreasonable, and the atomic spacing is too small. Most structural problems can be solved by appropriately modifying the torsion angle. In Sugar The protein test file contains examples of using the impose command to control the torsion angle.
Each subdirectory under GLYCAM contains tests related to a specific force field. To run a test, first save all relevant output files and intermediate files, then switch to the subdirectory and run the following command
./Run.GLYCAM evaluate
To restore the directory to its original state, run
./Run.GLYCAM clean
The 00_README file in the main directory contains more information about the test.
When the sequence command is used in LEAP to connect monosaccharides to form linear oligosaccharides (similar to generating polypeptides), the order of residues is opposite to the standard convention for writing residue sequences.
For example, to build graph disaccharides, use the sequence command of LEAP, the format is
upperdisacc = sequence {ROH 3GB 0GB}
lowerdisacc = sequence {OME 4GB 0GA}
Although the sequence command is the most straightforward way to construct linear polysaccharides, it is not the only way. A very convenient way is to use the GLYCAM online tool http://glycam.ccrc.uga.edu or http://www.glycam.org.
Linear oligosaccharide construction tutorial
This section shows how to create a simple straight chain tetrasaccharide
α-D-Manp-(1-3)-β-D-Manp-(1-4)-β-D-GlcpNAc-(1-4)-β-D-GlcpNAc-OH
The first step is to determine the GLYCAM residues used to construct this oligosaccharide.
Reverse the sequence order for use in the sequence command of LEAP:
Residue name sequence: ROH 4YB 4YB 3MB 0MA
Residue number: 1 2 3 4 5
The following LEAP instruction is used to construct the above sequence (of course, other methods can also be used to do it)
source leaprc.GLYCAM_06j-1 # Load leaprc
glycan = sequence {ROH 4YB 4YB 3MB 0MA} # Construct oligosaccharide
Use the sequence command, the φ angle will be automatically set, and its orientation is based on the prediction of the anomeric effect (±60°). If you want to change the torsion angle between two residues, you can use the impose command.
impose glycan {3} {{C1 O4 C4 H4 0.0}} # Set the psi between 4YB (3) and 4YB (2)
impose glycan {4} {{C1 O4 C4 H4 0.0}} # Set the psi between 3MB (4) and 4YB (3)
Now you can generate coordinates, topology and pdb files:
saveamberparm glycan glycan.top glycan.crd # save top and crd
savepdb glycan glycan.pdb # save pdb file
* For Research Use Only.
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