Building Libraries for VMD

Now, a detour. There are few libraries you will have to build. These are part of the standard VMD distribution but not part of VMD proper. They are:

libg++

These are modified versions of the GNU String and Regex classes. Their names are somewhat altered so there isn't a conflict with the original g++ distribution. To compile libg++ for a given architecture:

  cd ./lib/libg++
  -- Edit the Makefile and set the appropriate values for CC and CXX
  make clean
  make configure
  make
  -- if needed: mkdir lib_$ARCH  (e.g.: mkdir lib_IRIX5)
  mv libg-plus-plus.a lib_$ARCH
  -- for example: cp libg-plus-plus.a lib_LINUX

STRIDE

STRIDE is used by VMD to compute the secondary structure given the protein 3D coordinates. The appropriate STRIDE binary is included in the VMD binary distribution. To compile it yourself, see the web site at
http://www.embl-heidelberg.de/stride/stride_info.html for information on how to get the source and see ./lib/stride for information on how to use it with VMD.

Change line 43 of stride.h from

   #define MAX_AT_IN_RES             50

to

   #define MAX_AT_IN_RES             75

because there are many structures with non-standard residues containing more than 50 atoms.

Change line 96 of stride.c from

   return(SUCCESS);

to

   return(0);

since a program should return 0 if everything ended correctly.

Babel

Babel is used to convert different file formats automatically into PDB files(s) before reading them into VMD. Babel is a freely available general purpose molecular file conversion program. See the web site http://mercury.aichem.arizona.edu/babel.html for more information about it. This program must be available on the path somewhere or you can set the BABEL_BIN environment to point directly to the binary.

LASSP Tools

Some of the LASSP tools are used for computing matrix eigenvalues, determinates and inverses (needed for best-fit structure alignment). The code can be found at
http://www.lassp.cornell.edu/LASSPTools/LASSPTools.html . See the README in ./lib/LASSP for information on how to use the LASSPTools with VMD.

Renderers

VMD supports many types of rendering formats. You may want to get the packages associated with them. They are (among others) Raster3D, Radiance, and POV-Ray. Information about these and other programs can be found at:
http://www.ks.uiuc.edu/Research/vmd/software.

xmgr

The Labels form allows you to call an external program to graph a selected geometry value over time. The default program, which we suggest using, is xmgr, available from
http://www.ccalmr.ogi.edu/CDF/xmgr.html