A few suggestions :
First, I would not expect a sp3 hybridized atom to have a planar geometry.
Look at your input coordinates and make sure this is what you mean.
Second, check the atom type for this atom and look at the parameters.
Third,
There are more differences in your frcmod inputs than just ff14SB and
99bsc0. Isolate your variables.
If carefully checking all of these does not help, respond with more
information such as which atom mames in which RNA residue are having the
problem, the source of your input coordinates, and which exact frcmod
change is connected to the problem.
On Feb 1, 2016 11:15 PM, "Prayagraj Fandilolu" <fprayagraj.gmail.com> wrote:
> 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 Tue Feb 02 2016 - 04:30:05 PST
