Hello Amber experts and Dr. Miao,
I recently came across this paper "
https://pubs.acs.org/doi/10.1021/acs.jcim.3c01454" and was curious if the input files and a test folder could be shared with the community. I am excited to test LiGaMD on this system but I would love to access any input files that may help me setting up the system. One quick question I also have is I am working with 1EHT (NMR structure) and obviously the Mg ions are not resolved here.
Should I place the Mg ions based on close homologs in RCSB or should I strip all ions and weakly restrain the backbone of the RNA?
Many thanks
Debarati
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Received on Tue Feb 11 2025 - 09:30:02 PST
