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Hi,
I am optimizing dihedral parameters for modified RNA nucleotides. I would like to request suggestions regarding following protocol.
1.
I am using RNA OL3 to generate lib file, but I see C5’ atom is not assigned to atom type CI as expected. I am using following script :
#############
source leaprc.RNA.OL3
UFT = loadmol2 UFT-fragment.mol2
set UFT restype nucleic
set UFT name UFT
set UFT head UFT.1.P
set UFT tail UFT.1.O3'
saveoff UFT UFT.lib
quit
###############
1. Also, I am generating frcmod from mol2 file with parmchk2, however this also assigns CT atom type to C5’.
parmchk2 -i residue.mol2 -f mol2 -o nuclib.frcmod -frc ol3
1.
The parameters with penalty score > 50 and/or “ATTN” need reparameterization, is this correct? I see penalty score of 218.5 for some of the torsions.
1.
I have Gaussian scan generated coordinates in MOL2 format, is it possible to convert these to mdcrd to use with PARAMFit with AmberTools utilities? As I wish to correct E_QM energies with E_MM_without_torsion_energies for dihedral parameterization.
Sorry for multiple questions, I hope to receive suggestions from the community.
Thanks in advance,
Mandar
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Received on Thu Feb 19 2026 - 00:30:03 PST
