Dear Bill,
Here are the mdin files. The secondary structures of this ssRNA were predicted using several web based software. The predictions explained or partially explain the resullts we obtained from the experiments. But, those predictions can not generate coordinates for each atom.
Recently, I used iFoldRNA to predict the secondary and teriary strcutures of this ssRNA. This prediction somehow explained what we found from the lab. I tried to do MD simulation on the structure predicted from iFoldRNA. The pdb file predicted by iFoldRNA is also attached.
This question has bothered me for two to three weeks. Actually, I looked at the manual and amber archive. But I did not pay attention on NMR restraints and cartesian restraints. I will look into it, but may have questions later.
Many thanks,
Wu
----- Original Message -----
From: "Bill Ross" <ross.cgl.ucsf.EDU>
To: amber.ambermd.org
Sent: Monday, May 30, 2011 8:43:49 PM
Subject: Re: [AMBER] hold H-bonds of ssRNA fixed
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 30 2011 - 19:30:02 PDT
