From: Wen Li (liw_at_wadsworth.org)
Date: Thu Mar 31 2005 - 12:26:20 CST
Dear Dr. Stone,
Thanks for your message. I wonder which types of potential problems I
should look for in this case.
Thanks,
Wen
On Thu, 31 Mar 2005, John Stone wrote:
>
> Wen,
> The RMSDTT plugin is different, it'll be named 'rmsdtt' in the menu.
> I believe you got the directories right, but you may have a different problem,
> which is why I asked what you get when you type "package require rmsdtt",
> that should yield an error if something isn't working correctly...
>
> John
>
> On Thu, Mar 31, 2005 at 11:32:51AM -0500, Wen Li wrote:
> > In addition, Extensions/Analysis/RMSD calculator/RMSD Tool was in the vmd
> > before added rmsdtt. I wonder if I put the updated rmsdtt in wrong dir -
> > where is the right place to add?
> >
> > Thanks,
> > Wen
> >
> > On Thu, 31 Mar 2005, Wen Li wrote:
> >
> > > 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
> > > >
> > >
>
> --
> 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
>
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