> I am interested in doing MD simulation for a GC-rich ssRNA
> fragment, which have several internal H-bonds between base
> pairs. I did MD simulation by following the tutorial 1 in
> the Amber website. But, at the end of the simulation (with
> Na+ and explicit solvent), the internal H-bonds are separated.
>
> My question is
> How to hold H-bonds of base pairs fixed, and perform MD
> simulation for the rest atoms?
How long did you run each phase of equilibration? It would also help
if you included all the mdin files. Were the hbonds conserved during
equilibration?
Assuming your equilibration was good, you could consider adding NMR
restraints to supplement the hbonding potential. These are described
in the manual. This wouldn't necessarily keep the bases planar; to do
this would involve putting cartesian restraints on the bases in question,
also described in the manual, but this might overly constrain the whole
system - it depends on what you want to achieve.
Bill
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Received on Mon May 30 2011 - 19:00:04 PDT
