VMD-L Mailing List

From: Alexander Adams (xadams_at_umich.edu)
Date: Wed Apr 29 2020 - 14:30:31 CDT

Thank you all for your assistance. I am on macOS, so I've opted to use pbc
unwrap in PBCTools to solve the problem. I will hold onto these other
solutions but can proceed with PBCTools unless something changes. Thanks
again!

On Tue, Apr 28, 2020 at 4:20 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
> 

-- 
University of Michigan, Ann Arbor
Ph.D. Candidate - Mayes Lab
College of Engineering - Chemical Engineering