Dear AMBER developers/support team:
I am simulating a nucleosome (DNA+histone octamer) with oligosaccharides.
My input pdb file consists of 30 disaccharides (glycam ff), nucleosome with
DNA + proteins+ cocrystallised ions and conserved water. I have solvated
the system using an octahedron TIP3P water box and also included ionic
strength.
I tried doing autoimage and stripping ions, water and explicit solvent but
a few of the proteins do not get imaged correctly. I thought of doing image
centre/origin but it didn't help. Should I image on the DNA? I appreciate
any feedback that you might have for working with this system.
Many thanks,
Neha
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Thu Aug 04 2022 - 13:30:13 PDT
