[gmx-users] Superpositioning small molecules

[David]

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
> > PRODRG)
> 
> 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.
________________________________________________________________________
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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