[gmx-users] Superpositioning small molecules

David spoel at xray.bmc.uu.se
Fri Jan 9 22:18:01 CET 2004

On Fri, 2004-01-09 at 22:04, Anton Feenstra wrote:
> Daan van Aalten wrote:
> > Hi Anton
> > 
> > PRODRG currently reads in MOL2 files and writes out the GMX .gro and .itp
> > files. Note that MOL2 files not only contain coordinate information, and
> > converting MOL2 *topology* information to GMX atomc types etc. or writing
> > it out is not trivial (I've spent the last 7 years optimising this in
> OK, that is certainly an issue to consider. It would still be good to start
> with at least reading the coordinate data from mol2, that isn't hard to do.
> Also, it could be required to give a valid mol2 file as input if you want
> to write mol2 files, in that case one can 'substitute' the coordinates and
> leave the topological information untouched. That, at least, will be a
> start and would server many of the desired purposes.
If something, for coordinates we should implement a CML reader. CML is
available through openBabel, and many programs can read it. I don't know
the mol2 format, but if it does combine topology and coordinates, and if
I interpret Daan correctly, it is not the way to go. 

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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