Date: Fri, 25 May 2001 05:34:41 +0000
From: samantha hughes
Subject: Re: Amber, VMD and visualization

Dear Hermann

VMD reads in AMBER format topology and mdcrd (or .rst) files with
no modification necessary. Download and install VMD and you will
see its very interactive and easy. No piping or scripts
necessary.

VMD site
http://www.ks.uiuc.edu/Research/vmd/

The only problem you might encounter is if you have a very big
system (of the order of 90 000 atoms). If you do have
difficulties, you can contact me and I will tell you how we get
around this.

Good luck!


Samantha



> 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?
> What about using gOpenmol? Has anybody used that?
> Please point us in the right direction. Any suggestions would be gratefully
> appreciated.
> Thank you very much.
> Hermann von Grafenstein and Harsh Parikh.