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Date: | Fri, 3 Mar 2017 18:02:12 -0500 |
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Hi Neha,
The prep files that were available did not include an open valence at the 4-position. I've adapted those prep files to create the 4-linked parameters (attached).
I noticed that the documentation incorrectly describes the linkage orientations for the glucosamine residues. The 4YN residue refers to the beta-linkage, whereas the 4Yn residue is alpha.
The following is an example tleap script that builds a repeating unit of beta-GlcNH2:
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#tleap input file
set default PBradii mbondi2
source leaprc.GLYCAM_06j-1
# Change the path for the prep to match the location on your system:
loadamberprep /home/david/prep_files/GlcNH2_and_GlcNH3_0-4_link.prep
# The file that I have attached connects to the O6 atom by default - this can be corrected by explicitly designating the O4 atom (this is a bug for 4YN, but 4Yn does not require the following line).
set 4YN tail 4YN.1.O4
# Create the glycan sequence, note that the sequence begins from the reducing end of the glycan
glycan = sequence { OME 4YN 4YN 4YN 4YN 4YN 4YN 4YN 0YN }
saveamberparm glycan chitosan.prmtop chitosan.rst7
savePDB glycan chitosan.pdb
quit
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Please let me know if you have any other questions.
Best,
David
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