AMBER Archive (2009)

Subject: [AMBER] Circular RNA topology file

From: Kasprzak, Wojciech (NIH/NCI) [C] (
Date: Wed Oct 21 2009 - 13:26:04 CDT


I am trying to prepare a circular RNA molecule (such as, for example PDB# 2OIU)
for an MD run. I was able to produce the prmtop and inpcrd files in xleap by
editing out the H5T, H3T and the RX5 and RX3 designations that xleap placed
there in the first pass (without removing the first (in the pdb file) nuleotide's phosphate
  RNA minimization worked fine, but during the equilibration in solvent the last-to-first
nucleotide backbone connection (O3' - P) "drifted apart," suggesting that the topology
file most likely is not correct.

Does anyone know the correct procedure I should follow, and, if so, could show
examples of the pdb and prmtop files.

Thank you, Voytek Kasprzak
Wojciech (Voytek) Kasprzak [Contractor]
Analyst Programmer,
Basic Science Program, SAIC-Frederick, Inc.
National Cancer Institute in Frederick, Frederick, MD
(301) 846 5537
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