You can use ptraj or cpptraj to do it. Load all of the structures in via
the "trajin" command, align them with an RMSD command, and then calculate
the average structure (which you can dump as a PDB or some similar file
format).
HTH,
Jason
On Tue, Jun 26, 2012 at 8:15 AM, Olena Dobrovolska <
olena.dobrovolska.biotech.ntnu.no> wrote:
> Hi everybody,
>
>
>
> Do you know how to calculate the average protein structure from the 20
> minimized conformers in AMBER?
>
> (I tried to make it in MOLMOL, but the obtained avemin structure contains
> extra atoms.)
>
>
>
> Thanks,
>
> Olena
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 26 2012 - 07:00:02 PDT
