Adding chemical derivatives to GLYCAM residues

These instructions apply to residues from GLYCAM06-h and later.  They also require that you use pre-existing residues in the GLYCAM prep file database.  However, there are brief notes regarding modifications of existing residues, if that is required.

The method for adding derivatives to GLYCAM residues is very similar to the method for building branched structures. The only complicated part involves determining the proper charge adjustment for the residue to which the derivative is added. The table below lists the available derivatives and other useful information. Please see the example below to learn how to use the information in the table.

Derivatization Code Link at1 Adjust charge on Charge adjustment
Acetylation ACX O bonded glycan C2 + 0.008
Methylation MEX O bonded glycan C2 – 0.039
Sulfation SO3 O linking oxygen + 0.031
N linking nitrogen varies3

1. “O” refers to a hydroxyl oxygen in the glycan. “N” refers to an exocyclic sp2 nitrogen.
2. The carbon atom bonded to the linking atom.  For example, if you link to O3, adjust the charge on C3, the carbon in the glycan that is bonded to the linking oxygen.
3. See explanation below.

Make sure you have a recent set of prep files and parameters.

  • The derivatives listed above are included in GLYCAM prep files beginning with version 06h.
  • Note that with version 06h, many atom type names have changed. For this reason, the 06h and later files are not necessarily compatible with earlier versions.
  • See to get the latest versions.

The following outlines our procedure for determining the best charge adjustment method.

The main GLYCAM residues are designed to be as modular as possible, yet still realistic. To this end, charges at linking atoms are adjusted so that they are always, effectively, +0.194 at each linking anomeric carbon and -0.194 at each linking oxygen. However, the derivatives in this tutorial differ sufficiently from glycosidic linkages that we were unable to retain realistic charges and the “0.194” modularity.  Rather than abandon the modularity altogether, we determined simple, alternative, charge alterations for each derivative.  The procedures were chosen so that builds remain uncomplicated and simulations results remain realistic.  To determine the best procedure for adjusting the charge, we investigated charge distributions from quantum mechanical calculations on ensembles of appropriate model compounds. This is how we determined, for example, that when adding a methyl derivative it is best to alter the charge on the next carbon over rather than on the linking oxygen.

Notes on the calculation of the charge adjustments in the table above:


  • These charge calculation instructions are intended for residues that are pre-configured for the proper branching combination.  See the O-sulfation example below regarding proper residue choice.  An example of a situation where the residue is not already available would be an aldofuranose with branches and/or derivatives at two positions, one of which is position 5 (because there are no letters assigned to multiply linked residues where one link is position 5).
  • If you must use a residue that is not already prepared for branching at the derivative location, you can still use these calculation instructions, but first you must pre-adjust the charge on the hydroxyl oxygen so that the modularity described above is maintained.  You will also need to remove the hydrogen.  Hydrogen removal should be done within tleap or xleap (or with similar knowledge of the file structure) and not by merely removing the hydrogen from the prep file entry.  The adjusted charge on the oxygen (adjOxCh) is: adjOxCh = oldOxCh + HydCh – 0.194, where oldOxCh is the oxygen’s un-adjusted charge and HydCh is the charge of the hydroxyl hydrogen to be removed.  The instructions below describe how to determine the further adjustment you need to make on adjOxCh, if any.
  1. Calculate the sum of charges (rCh) on the derivative residue.  This is merely the sum of charges on the derivative residue.  For example, for the sulfate residue, as of this writing, the sum is -0.837.
  2. Determine the formal charge (fCh) you would expect for the derivative.  The number here should be an integer.  For example, adding a sulfate (SO3) group brings a charge of -1.  Adding NH3+ would add +1.  Most derivatives, eg, methyl (CH3), will have fCh=0.
  3. Find the difference (dCh) between that and the formal charge (fCh) you would normally expect for the derivative. In the case of a sulfate group, the fCh should be -1.000. The difference, dCh=fCh-rCh, is -0.163, meaning that the glycan should carry that much of the sulfate charge.
  4. Find the charge inherent (iCh) in the glycan residue at the attachment point.  This step is different, depending on the type of linkage.
    1. For applying a derivative at a hydroxyl oxygen, the number is -0.194 because of the modularity mentioned above.  Note also:  You must use the GLYCAM residues intended for linking monosaccharides as described in the sulfation tutorial below.  That is, if you want to sulfate at O6, of alpha-D-Glcp, then use residue 6GA.  Do not use 0GA.  If there is not a residue for your situation, see the Notes above.
    2. For applying a derivative at the N in an N-acetyl group, add up the charges on the acetyl part.  The relevant atom names are typically C2N, O2N, CME, H1M, H2M, and H3M.  iCh will be the negative of that number.  For example, in the GLYCAM residue 0YB (beta-D-GlcpNAc), the sum is 0.106, so iCh is -0.106.  Note:  For N-sulfation, the charge alteration will be the same for each linkage variant (e.g., 0YB versus 6YB and WYB).  But, beta-D-GlcpNAc will need a different alteration than alpha-D-GlcpNAc and so forth.
  5. Find the difference between dCh and iCh.
    1. For example, when linking at an oxygen, dCh-iCh is 0.031.  So, you will need to add 0.031 to the glycan at every linking oxygen where a sulfate is attached.
    2. For the example using beta-D-GlcpNAc, dCh-iCh is -0.057, so you would add that to the linking nitrogen.

The following explains how to build an O-sulfated disaccharide.

      1. Determine the base GLYCAM residue(s) you need to use.
        To do this, first determine the total number of attachment points for each sulfated saccharide monomer. For example, if you wish to build a-D-Manp-(1-6)-b-D-Glcp-OH with sulfation on the glucopyranose at positions 2 and 4, then the residues you will need are ROH (the reducing end hydroxyl group), RGB (a b-D-Glcp linked at the 2, 4 and 6 positions) and 0MA (non-reducing end terminal a-D-Manp).
      2. Determine the amount to alter the charge at each sulfation point.
        See in the table above that the amount is +0.031.
      3. Alter the charge at each sulfation point.
        Check the table above to determine where the charge difference should be applied. In this case, the charge is applied to the linking oxygen. The example below shows how to alter the oxygen charges individually using xleap or tleap. If you are comfortable copying and altering the appropriate prep file entries, that is an acceptable alternative.
      4. Build up your molecule in a manner similar to any other GLYCAM structure.
        The example below should be reasonably explanatory.

Example input for tleap or xleap

## Load in the databases
source leaprc.GLYCAM_06 # or substitute a more recent leaprc 
loadAmberPrep sulfate.prep # as of 20110627, this is the file name 
## Create a unit containing the basic glycan
m = sequence { ROH RGB } # stopping here ensures no confusion about linkages
set m tail m.2.O6 # tell leap explicitly where to link
m = sequence { m 0MA }
# finish building the base glycan ##
## Set charges on the oxygens
##	You can use "desc m.2.Ox" to obtain the current linking-O charges
##	(here x=2 or 4).
## Here, we found them by reading the RGB entry in the GLYCAM_06.prep file.
##	The charges set below are the orignal charges altered by +0.031.
set m.2.O2 charge -0.445 ## was originally -0.4760
set m.2.O4 charge -0.437 ## was originally -0.4680
## Add sulfates to positions 2 and 4
set m tail m.2.O2
m = sequence { m SUL }
set m tail m.2.O4
m = sequence { m SUL }
## Check the charge to make sure it is -2.000 as we expect.
charge m
## Write out files we can use for simulations or to check our structure ##
saveamberparm m m.rst


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