[Chimera-users] chimera for Amber9

[Elaine Meng]

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