VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 28 2020 - 15:20:04 CDT

Hi Alex, you should use the same version of the Tcl library already linked
with VMD. In RedHat-based Linux distributions tcl-devel is the name of the
package to install. On Debian-based ones, tcl-dev. And so on.

Here are the instructions to build VMD:
http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html
You wouldn't have to build VMD itself: just use the same Tcl library used
in your build.

Since you mention Homebrew, are you on macOS? If so, things are definitely
more complicated (see threads about Catalina vs. previous versions on this
list). Also, take a look at PBCTools as well, which is quite a bit slower
than qwrap because it relies on scripted code, but should take you longer
than to troubleshoot how to link dynamically a plugin in macOS. This can
be done (again, see earlier messages) but it may not be time-efficient for
you.

Giacomo

On Tue, Apr 28, 2020 at 3:40 PM Ivan Gregoretti <ivangreg_at_gmail.com> wrote:

> Hi Alexander.
>
> As we wait for someone with experience to contribute with a solution
> for you, let me give you a pointer for you to start digging:
>
> If you do a Google search on "ld: symbol(s) not found for architecture
> x86_64" (with quotes) it will lead you to a stackoverflow.com post.
>
> The post is titled "g++ ld: symbol(s) not found for architecture
> x86_64" and I think that it might be useful for you.
>
> Ivan
>
>
> On Tue, Apr 28, 2020 at 2:09 PM Alexander Adams <xadams_at_umich.edu> wrote:
> >
> > Dear VMD community,
> >
> > I am working with gromacs trajectory files that show bonds stretched
> across the entire image due to PBCs. Previous vmd-l posts led me to the
> qwrap function repository, but I've had some trouble with installation.
> I've attached the errors I receive: error 1 when running with gcc and error
> 2 when running with clang. I haven't had much luck searching online for
> solutions to these errors and would appreciate any guidance that can be
> offered. I did see in a previous post that the package requires tcl devel,
> but I can neither find tcl-devel through homebrew or an internet search.
> Thanks in advance!
> >
> > Alex Adams
> > --
> > University of Michigan, Ann Arbor
> > Ph.D. Candidate - Mayes Lab
> > College of Engineering - Chemical Engineering
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin