VMD-L Mailing List

From: Wen Li (liw_at_wadsworth.org)
Date: Thu Mar 31 2005 - 10:24:18 CST

Hello Everyone,

I am trying to add "RMSDTT" plugin for VMD by doing the following that
results in loss of the VMD Main window without showing any error message
and rmsdtt can not be found in Extensions. When I remove .vmdrc in
/home/liw, the little window comes back. The following is what I did, and I
was hoping that you could help me to find what is the problem, thanks!

In as SGI:

1. mkdir
/usr/local/spider/vmd/vmd-1.8.3/vmd-1.8.3b4/plugins/IRIX6_64/tcl/rmsdtt

2. in the rmsdtt dir, add file pkgIndex.tcl which contains:
package ifneeded rmsdtt 1.0 [list source [file join $dir rmsdtt.tcl]]

3. in the rmsdtt dir, add downloaded file rmsdtt.tcl

now, in
/usr/local/spider/vmd/vmd-1.8.3/vmd-1.8.3b4/plugins/IRIX6_64/tcl/rmsdtt

ls -lt shows

-rwxr-xr-x 1 liw spider 535 Mar 31 10:20 pkgIndex.tcl*
-rwxr-xr-x 1 liw spider 37378 Mar 31 10:13 rmsdtt.tcl*

4. in /home/liw, add .vmdrc

lappend auto_path
{/usr/local/spider/vmd/vmd-1.8.3/vmd-1.8.3b4/plugins/IRIX6_64/tcl/rmsdtt}
if { [catch "package require rmsdtt" msg] } {
  puts "VMD RMSDTT package could not be loaded:\n$msg"
} elseif { [catch {menu tk register "rmsdtt" rmsdtt} msg] } {
  puts "VMD RMSDTT could not be started:\n$msg"
}

Wen

On Wed, 30 Mar 2005, John Stone wrote:

>
> Wen,
> You might want to check out Luis Gracia's "RMSDTT" plugin for VMD,
> as I believe it would do the alignment for you without much effort:
> http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/index.html
>
> Once aligned, it is easy to write out the new coordinates using
> 'mol writeXXX' and such.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Mar 30, 2005 at 04:21:26PM -0500, Wen Li wrote:
> > Hello everyone,
> >
> > I hope that you could help me on the following question with either vmd
> > or namd, or any program:
> >
> > I have an MD trajectory generated using AMBER, and I want to align
> > snapshots of this trajectory to the coordinates of a reference structure.
> > And then write out the coordinates of each aligned snapshots. Is this
> > doable in VMD?
> >
> > Thanks,
> > Wen
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>