Hermann von Grafenstein writes:
>Dear Amber experts,
>We are new to Amber. So far, we have managed to install Amber6 on Linux
>(Redhat 7). Now we would like to visualize (animate) energy minimization
>trajectories. As evident in the mail reflector, others have successfully
>used VMD for that purpose. What do we need to do, at the Amber end, for
>piping the coordinate outputs to VMD? And how do we build, at the VMD end,
>an interface that can accept output from Amber6? How can we get Amber to
>accept a connection request from VMD? How can we specify Amber to send the
>coordinates to a particular port? Does anyone have a Sander input file
>and/or a Tcl script for VMD?
Dear Dr. von Grafenstein,
I have written support for animation of AMBER6 trajectories
in MidasPlus and Chimera.
For MidasPlus, see
http://www.cgl.ucsf.edu/Outreach/midasplus/
then download the Movie delegate from
http://www.cgl.ucsf.edu/home/dek/Movie
(warning it's pretty old and no longer supported- and the Linux version
of MidasPlus on the CD is ancient- once you have obtained the license,
contact me and I can get you a version that is more up-to-date in terms
of OpenGL and Motif. 2-3 since MidasPlus was released on CD have been
"light years" in Linux development, and the backward compatibility was
broken along th away.)
For chimera, see
http://www.cgl.ucsf.edu/chimera
AMBER6 support is built-in to the latest release of chimera. Just call
up "Molecular Dynamics->Movie" from the Extensions menu, and load a
prmtop/prmcrd or traj file.
Note, the releases of chimera on the web site only work with Red Hat
6.2 (and debian 2.2, and other compatible distributions) not Red Hat
7. You shouldn't use Red Hat 7.0 at all, Red Hat 7.1 is more stable
and reliable. We will be releasing a RH7.1- compatible version of
chimera iwth the next release, along with 6.2.
Dave
Received on Thu May 24 2001 - 19:03:13 PDT
