On Thu, Feb 25, 2010 at 11:21 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>> Also is there any way to compare 2 PDBs structurally, and calculate
>>> similarity in Amber or any other free software?
>>
>> RMS is certainly one way to quantify structural similarity. This can
>> be done in ptraj or vmd or pymol or any number of other visualization
>> programs I'm sure.
>
> This applies to chemically identical structures. There must be more
> general indices of similarity.
I think only the selected masks must be identical. I know that VMD
will align structurally similar systems as long as the selection
across both systems is identical. I'm not sure if ptraj operates the
same way or not, but I imagine it might if you just feed it two PDBs.
>
> Bill
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 25 2010 - 21:00:03 PST
