VMD-L Mailing List

From: Pablo De Biase (pablodebiase_at_gmail.com)
Date: Tue Nov 22 2011 - 13:38:58 CST

I have found a solution to your problem and mine. Something has changed
from previous version of ubuntu to ubuntu oneiric. I think it may be the
csh. Now is using a new version. rlwrap version seems to be the same.
To fix this issue edit vmd run script (/usr/local/bin/vmd). If you use "vi"
just do:
sudo vi /usr/local/bin/vmd

look for rlwrap doing in vi "/rlwrap"
there you will see this:

 # detect if we have rlwrap available to have commandline editing
set vmdprefixcmd=""
if (("${ARCH}" == "LINUX") || ("${ARCH}" == "LINUXAMD64")) then
  set rlwrap=`which rlwrap`
  if ( -x "$rlwrap" ) then
    if ( -f ${MASTERVMDDIR}/vmd_completion.dat ) then
      set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ -f
${MASTERVMDDIR}/vmd_completion.dat "
    else
      set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ "
    endif
  endif
endif

Apparently, csh cannot understand the symbols as they are: (){}[],&^%#;|\\
Probably a slash (\) is needed before some symbols now.
I just fix it removing the -b option because the default options are those
symbols. So comment both lines and replace by the same line without b
option and without symbols as I did below. That fixes the issue.

# detect if we have rlwrap available to have commandline editing
set vmdprefixcmd=""
if (("${ARCH}" == "LINUX") || ("${ARCH}" == "LINUXAMD64")) then
  set rlwrap=`which rlwrap`
  if ( -x "$rlwrap" ) then
    if ( -f ${MASTERVMDDIR}/vmd_completion.dat ) then
# set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ -f
${MASTERVMDDIR}/vmd_completion.dat "
      set vmdprefixcmd="rlwrap -C vmd -c -f
${MASTERVMDDIR}/vmd_completion.dat "
    else
# set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ "
      set vmdprefixcmd="rlwrap -C vmd -c "
    endif
  endif
endif

On Nov 1, 2011, at 11:50 AM, Frank Barry wrote:
> I am having problems running vmd 1.9 on a newly installed Ubuntu box.
>
> $ vmd
> rlwrap: No match.
>
> I found this related posts on the list:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/18099.html
>
> As in the post, if I comment out the "rlwrap block" in the start-up
script I can get vmd to open but with quite poor performance (maybe
unrelated).
> I am quite new to Linux (especially Ubuntu). So any tips on a better way
to proceed would be helpful.
> Thanks in advance,
> Frank
>
>
> ## using vmd-1.9.bin.LINUXAMD64.opengl.tar.gz
>
> $ which csh rlwrap
> /bin/csh
> /usr/bin/rlwrap
>
>
> $ ./configure
> using configure.options: LINUXAMD64 OPENGL FLTK TK ACTC CUDA IMD LIBSBALL
XINERAMA XINPUT LIBTACHYON VRPN NETCDF TCL PYTHON PTHREADS NUMPY SILENT
>
> $ cd src/
>
> $ sudo make install
> Make sure /usr/local/bin/vmd is in your path.
> VMD installation complete. Enjoy!
>
> $ vmd
> rlwrap: No match.
>
>
> $ head /usr/local/bin/vmd
> #!/bin/csh
> set defaultvmddir="/usr/local/lib/vmd"
>
>
> $ uname -a
> Linux perutz 3.0.0-12-generic #20-Ubuntu SMP Fri Oct 7 14:56:25 UTC 2011
x86_64 x86_64 x86_64 GNU/Linux
>
>
> $ lsb_release -a
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description: Ubuntu 11.10
> Release: 11.10
> Codename: oneiric
>