[gmx-users] Superpositioning small molecules

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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