[Chimera-users] chimera for Amber9

Francesco Pietra chiendarret at yahoo.com
Tue Oct 2 03:12:15 PDT 2007

Hi Elaine:
That you mention was wonderful discovery.

Coming closer to my work: What I want to do at the moment is examining if Dock
can identify how certain natural products (lipophilic molecules of about 180
first-row atoms) interact with a large protein. I know experimentally that
there is interaction, nearly surely with the protein itself and not merely a
destruction of the bilayer. Though, I have no idea about the protein region
I have already carried out a conformational search for my natural products by
simulated annealing with an algorithm that calls Amber9. Parameter and
coordinate files for Amber9 were built with Antechamber. X-ray diffraction data
at medium resolution for the protein are available.

The tutorials on DOCK does not consider take such a problem (the tutorial
starts from a protein-ligand complex elucidated by X-ray diffraction).
Professor Brozell suggested that the size of the protein may put a practical
limit on the size of Dock's grid, though, one approach would be to divide and
conquer the big protein binding sites into subsets that would be processed

My question is: can Chimera help such preparation of the protein for docking?


--- Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> Thanks for your kind words!
> Yes, you can view AMBER trajectories in Chimera.  Just start "MD  
> Movie" (under Tools... MD/Ensemble Analysis) and in the resulting  
> dialog, there are several choices for trajectory format, including  
> Amber.
> The MD Movie tool and input formats are described here:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ 
> framemovie.html
> and are used in this tutorial:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
> ensembles2.html
> The trajectory input types are not listed in the general "file open"  
> dialog, partly because some formats include more than one file.   
> Also, the more specific MD Movie dialog allows you to specify other  
> parameters, such as the range of frames you want to load.  I hope  
> this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Oct 1, 2007, at 6:22 AM, Francesco Pietra wrote:
> > Having installed DOCK6.1/DMS (debian Linux parallel amd64) and  
> > Chimera 1.2422
> > (scp-linked desktop Debian Linux i386), may I ask:
> >
> > 1) Can I use Chimera for Amber9 in place of VMD, which I currently  
> > use?
> >
> > 2) Being superficially familiar with VMD, I was looking in Chimera  
> > for *.prmtop
> > and *.inpcrd file types, as well as rst file, etc.. I suppose I was  
> > unable to
> > turn Chimera to use with Amber9.
> >
> > That said, I was very much impressed by Chimera at the first touch.
> > Thanks
> > francesco pietra

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