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Problem with sugar parameters

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Problem with sugar parameters

Hi, everyone.

I encountered a weird relax-optimization output in a structure containing sugars. The output structure has hydrogens in close contact (~1.2 Å) from a sugar molecule and a serine residue. In this reported case, I use the -include_sugars flag, but I've observed the same behaviour with custom params generated for glucose in another system, in which I found hydrogens in close contact with a tyrosine. It seems to be an issue of the Hpol atom type, which allows this to happen for a hitherto unidentified reason. The attached relaxed PDB (truncated at the C-terminus to fit the 512kb limit for uploading, which is a bit low for PDB if you ask me) shows the interaction between hydrogens from residue GLC5 (chain B) and SER105 (chain A).

Any clue on this behaviour will be appreciated.


hydrogens_kissing.png444.28 KB
1BAG_relaxed.pdb511.3 KB
Post Situation: 
Sat, 2023-10-07 10:17
Martin Floor