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Software contributions to download

New site! this page is no longer actively maintained.

There is now an independent site focusing on software development, downloads etc. It contains everything that was on this page and much more. Access to this site is via http://baaden.free.fr/soft.

top2psf - convert Gromacs topology files to PSF files usable by VMD

This is a perl script to convert a Gromacs topology file (.TOP/.ITP) or alternatively a PDB file with Connect records in a Charmmm/Xplor psf file using the information about atom types, charges, masses and bonds. Then one can use VMD to visualize pdb+psf and verify whether the bonding topology is ok. It is based on the gmx2mmc script by Graham Smith.

If you try to use the script on a complex system (more than just a protein, maybe some lipids plus water and so on), then you should use the preprocessed topology file, i.e. the one you get from using grompp's -pp option.

The script is available from the VMD Script Library (direct link top2psf) or from this server (top2psf).

gmx_rescue - recover corrupted Gromacs trajectories (xtc files)

This is a utility to rescue partly corrupted XTC files. It works under Linux and is based on earlier files contributed for SGI (see README.rescue). The actual files are called gmx_rescue.c and README.rescue. O. Beckstein has added large file support for linux.

This tool came in handy for me because a lot of simulations that I had run on some supercomputer had corrupted XTC files (apparently due to hardware problems or NFS errors). Rescuing them made me (up to now) just loose about 10 frames in 2500, so I think this is still acceptable and avoids re-running the simulations.

The script is available from the Gromacs Software Contributions (direct link gmx_rescue.tgz) or from this server (gmx_rescue.tgz).

VRPN Library v06.03 with Phantom support for SGI and GHOST 3.1

This version of the VRPN (Virtual Reality Peripheral Network) library is an adaptation in order for the Phantom server to run on SGIs using GHOST 3.1 (nowadays support for Phantom under SGI is stopped). I haven't tested whether the changes that I have contributed still work for more recent versions of the library.

Making the necessary changes in the library wouldn't have been possible without the invaluable help of David Marshburn, Adam Seeger, John Stone and Russell M. Taylor II.

The tarball of the modified version can be downloaded from this server (VRPN v06.03 tarball).

Opera bookmark to XML converters

There are two perl scripts to convert and manipulate Opera bookmark files. They are an extension of the op2xbel script originally written in Python by Lars Marius Garshol and rewritten in perl by Briac Pilpréby. On one hand the script was modified to extract a complete subfolder of a huge opera bookmark file (op2self). On the other hand, one can export into a docbook conforming XML document instead of Opera adr to xbel conversion (op2docbook). The docbook XML source can then eg be included as a chapter or so in a docbook documentation.

The scripts are available from this server (op2self, op2docbook).