Dear Amber users,
I am simulating a RNA system using the ff14SB in Sander. I am facing an
issue with SP3 planar nitrogen atoms of my system. After minimization, the
orientation of planar SP3 Nitrogen is changing and its planar conformation
is lost.
I have checked the same system with older ff99bsc0. This ff works fine and
the SP3 planar nitrogen atoms are still planar after minimization.
I am not getting a clue into this...
can some one give me a solution to this issue????
Other parameters being loaded with ff14SB are:
frcmod.modrna08
frcmod.chiOL4
frcmod.ionsjc_tip3p
while in case of ff99bsc0 i am using:
leaprc.rna.ff99
leaprc.ff99bsc0
frcmod.ol.dat
What is the reason of this??
Mr. Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
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Received on Mon Feb 01 2016 - 20:30:04 PST
