[AMBER] fixing backbone dihedral angles in RNA structure

From: Asmita Gupta <asmita4des.gmail.com>
Date: Thu, 10 Aug 2017 17:58:58 -0700

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?


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Received on Thu Aug 10 2017 - 18:00:04 PDT
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