Downloads

In order to use these libraries for production of topology and coordinate files to be further used for AMBER simulations do the following in tleap or xleap:

  1. Source GLYCAM06 force field: source $AMBERHOME/dat/leap/cmd/leaprc.GLYCAM_06j-1
  2. Load the library (LIB.lib) you need: loadoff LIB.lib
  3. Now you can either use sequence command to build your GAG: new_unit=sequence { … LIB …}
  4. Or you can read the data from the pdb: new_unit=loadpdb my_pdb.pdb

Note on Ido2UA residues: If you want to build a molecule which contains Ido2UA, pay attention to the fact that this residue rather exists in 1C4 and 2S0 conformations. In our libraries, ALL residues are in 4C1 conformation. Therefore, DO NOT use sequence command for these. Instead use the prepared heparin dp10 files with Ido2SUA in 1C4 and 2S0 conformations and read them by loadpdb command.

Non-terminal residues (in glycosidic linkage)

References: 1. Case DA et al. AMBER 14. 2015. 2. Kirschner K et al. GLYCAM06. J. Comput. Chem. 2008;29:622–655. 3. Huige C, Altona C. J. Comput. Chem. 1995;16:56–79.

Docking GAGs with Autodock 3

Download prepared GAG ligands for AD3. The charges are assigned with the use of the GLYCAM06-compatible libraries accessible above.

Abbreviations: HE: heparin (1C4 conformation of IduA(2SO)), DS: dermatan sulfate, CS: chondroitin sulfate, HA: hyaluronic acid, deHE: desulfated heparin, pHA: persulfated hyaluronic acid, dp: degree of polymerization.

In our AD3 protocol we usually obtain 1000 solutions that are further clustered and analyzed. Modified parameters:

ga_pop_size 300
ga_num_evals 999500000
ga_num_generations 10000

Biomolecular Modelling: Methodology and Case Studies

Introduction to Molecular and Cellular Biology