On Sat, Mar 05, 2016, Sreemol G wrote:
> I have PDB structure of RNA molecule. in that adenine, guanine, cytosine
> and uracil are named as ADE, GUA, CYT and URI respectively. while loading
> it in xleap i got the message "unknown residues:" and "created a new atom
> named: O2 within residues: ... etc".
This is (somewhat) surprising. The standard leaprc file (like leaprc.ff14SB)
translate old-style PDB residue nomenclature (like ADE,GUA...) into deoxy
residues (DA,DG...). You can change this to RNA by looking at the comments at
top of the leaprc file.
It would be most helpful to know what leaprc files you are using, and what the
*exact* error message is. You could get an "unknown residue" error if you
really have URI residues, since even the old PDB standard called uracil
"URA", not "URI".
As Vlad suggested, probably the simplest thing is to just change the residue
names to the current PDB/IUPAC standard.
....dac
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Received on Sat Mar 05 2016 - 07:00:03 PST
