Dear all,
One of our group members posted a question that, unfortunately, did not
appear on the mailing list. Kindly give your suggestions. I am reposting
the same.
We have added a phosphate group to the 5' end of a uridine residue in a
nucleic acid duplex. The uridine is the terminal residue at the 5' end of
the duplex. We optimized the structure and performed ESP charge fitting of
the phosphate-modified uridine residue using Gaussian. Subsequently, we
used Antechamber and tleap to generate the force field parameters.
During the equilibration step of my MD simulation, we encountered a "vlimit
exceeded" error. Upon analyzing the trajectory, we noticed that the base
pairing at one terminal of the duplex is completely disrupted during
equilibration.
I would greatly appreciate any suggestions for resolving this issue.
Additionally, does anyone know if there are frcmod and prepin/mol2 files
available for the 5' phosphate-modified uridine residue on the RED Server
or elsewhere?
Thank you for your time and help!
Regards,
Sruthi Sudhakar
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Received on Mon Nov 25 2024 - 04:30:02 PST
