Re: vmd-l: conformational alignment

From: Wen Li (liw_at_wadsworth.org)
Date: Thu Mar 31 2005 - 10:32:51 CST

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
> >
>

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