Date: Wed Jun 02 2021 - 07:44:06 CDT
I have a glycoprotein complex (pentasaccharide) bonded to a flavonoid ligand, which also has a D-glucose group.
I used the Charmm-gui webserver to generate the inputs for namd.
For the protein-oligosaccharide group it worked very well.
However, the interface automatically recognizes the D-glucose group of the ligand and deletes the rest of the flavonoid.
Ideally, the interface would have the option of not modeling the glycan group for a given chain. In this case, I would upload the ligand's force field, but this is not yet possible.
My question is: Does anyone have any tips on how I could generate the .psf and .coor files for this glycoprotein-flavonoid complex?
NOTE: I have already generated topology and parameter files for the flavonoid.
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