VMD-L Mailing List

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Wed Sep 16 2009 - 14:21:00 CDT

I wrote a script, where you can give a range of resid IDs, but the
rotation will be such that you always rotate two rigid bodies, separated
by the particular dihedral angle you change.

Would that help?
Sebastian

Peter Freddolino wrote:
> Hi Jorgen,
> I'm not aware of a simple solution; you'll have to write a little
> procedure for it. You should be able to copy most of the code from
> ::Molefacture::rotate_bond (in molefacture_geometry.tcl). Just feed in
> your atom indices instead of using the dihedatom array, and don't bother
> with the stuff at the end that updates the molefacture graphics. The
> selections for atoms on the two sides of the dihedral are calculated in
> the highlight_bond proc of molefacture_internals.tcl, which uses
> ::util::bondedsel.
> Best,
> Peter
>
> Jorgen Simonsen wrote:
>
>> Hi all,
>>
>> I would like to rotate the dihedral angle of one of my residues from
>> 60 to 120 with 10 degrees interval. I have been looking at the
>> molefracture but would like to invoke it form the command line. I am
>> not quite sure how to proceed if my atom names are c1,c2,c3,c4(they
>> have a dihedral angle in the moelfracture) how to change the angle by
>> steps of 10 using vmd command line?
>>
>> Thanks in advance
>>
>> Best
>>
>> Jorgen
>>
>
>