Date: Tue, 23 Sep 2025 09:08:47 +0000
Dear Amber community,
I am making a co-solvent system with mono and disaccharides. My approach for monosaccharides is use parmed to change the Os - Os LJ potential, to induce inter-glycan repulsion at large distances using
changeLJPair .%Os .%Os 10.0 0.0001
This keeps the monosaccharides out of hbonding distance preventing aggregation at high concentrations. It appears to work quite well.
I am now working on disaccharides. I chose the glycosidic linkage oxygen as my repulsive atom and tried using
changeLJPair .%Os&.O3 .%Os&.O3 15.0 0.0001
There is only one Os atom that is named O3, so I thought this would work. The only other Os atoms are named O5. What is strange to me (hopefully not to you) is that this works for one of the O5 atoms (on a second monosccharide of the disaccharide), so no repulsion is seen, however on the other O5 atom (the same residue as the O3 atom) the O5 is repelled and the glycan geometry is malformed.
I tried negative selection with the same outcome.
changeLJPair @%Os&!.O5 @%Os&!.O5 15.0 0.0001
Does anyone know why this is the case and have a possible solution? I could try giving the O3_Os atom a completely differnent name but it would be nicer to get this working as the approach is simpler.
Many thanks
Dr James Ross
EPSRC Synthetic Biology Research Fellow,
School of Molecular and Cellular Biology,
Astbury Building 7.107
University of Leeds, UK
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