Similar to what Bill recommended, the 'rotatedihedral' command in
cpptraj can be used to rotate dihedrals by increments or to a certain
value. For example, to rotate the chi (nucleic) torsion in residue 8
to a value of 35 deg.:
parm myparm.parm7
loadcrd mycoord.rst7 name MyCoord
rotatedihedral crdset MyCoord value 35 res 8 type chin
-Dan
On Thu, Aug 10, 2017 at 9:08 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> You can look into the 'impose' cmd in leap. I suspect it isn't used
> much, but it is intended to address this issue.
>
> Bill
>
>
> 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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>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Aug 11 2017 - 10:30:04 PDT
