Hi,
I was trying to set up a with RNA. With the wildtype RNA structure, I was able to prepare a system using tleap. I was also trying for some modification in C7 of RNA. The C7 of wildtype RNA is modified into N3(H+) cytidine in order to stabilize the triple base stacking.
I found a paper suggesting renaming C7 to "CP" and using parameters for N3(H+) cytidine from the residue name ‘CP’ from all_prot_nucleic10.lib in Amber 18. I am using AMBER 20 for my system preparation. I followed the instructions in the protocol of the paper; however, I ran into issues with bond and angle parameters. I tried using antechamber and tleap to generate .frcmod file using all_prot_nucleic10.lib, the issue still persists. I was wondering if anyone could help me with suggestion on how to deal with the issue.
Kushal Koirala
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Received on Mon Sep 18 2023 - 16:30:02 PDT
