Dear all,
We are working on an oxepane derivative and want to do a simulation
wherein we replace the deoxyribose sugar of dA to oxepane in 1BNA and
perform a test simulation. We have carried out the following procedure for
the same. However, we get a really distorted incorporation. We request you
to kindly suggest any errors in the methods or any related suggestions.
1. Retrieved the structure of the nucleoside from a crystal structure and
added phosphate capping at 3' and 7' position (it has a 3'-7' linkage).
Performed optimization and esp calculation followed by resp fitting
2. Removed the phosphate capping, matched the atom names and added the
residue name into 1bna template.
3. Loaded into tleap with parmbsc1 force field and the frcmod generated
after resp fitting.
but the phosphate linkages are not proper and a lot of steric clash is
occurring. Any suggestion or detailed protocol on how to incorporate
modified nucleotides will really be helpful.
Regards,
Sruthi Sudhakar
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Received on Wed Feb 07 2024 - 04:00:02 PST
