Re: [AMBER] fixing backbone dihedral angles in RNA structure

From: Bill Ross <>
Date: Thu, 10 Aug 2017 18:08:23 -0700

You can look into the 'impose' cmd in leap. I suspect it isn't used
much, but it is intended to address this issue.


On 8/10/17 5:58 PM, Asmita Gupta wrote:
> Dear users,
> I am trying to build a model RNA structure consisting of a 10 base-paired
> helix with 6 residue long 5'-dangling/single-stranded sequence. For this
> purpose, I used "fuse" command in PYMOL to create a bond between 3' end of
> single stranded chain and 5'-end of helix. The resulting structure needs to
> be positioned with respect to an RNA helicase in such a way so as to avoid
> steric clash. Manually docking the RNA structure is causing bad dihedral
> angles to creep up in the model.
> Is there any way to remove or correct such angles during minimization for
> getting a reasonable starting structure for simulation?
> Thanks,
> Asmita
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Received on Thu Aug 10 2017 - 18:30:02 PDT
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