[gmx-users] Topology builder

[David van der Spoel]

Erik Lindahl wrote:
> Hi,
> 
> There are a couple of programs out there (e.g. Macromodel) that tries to 
> do this, even for OPLS, but they fail miserably way too frequently. I've 
> even seen cases where the autogenerated topology was reported as "likely 
> high quality", but the small molecule didn't even have unit charge and 
> the atom types were simply not correct.
> 
> Having said that, this functionality is implemented in the x2top tool, 
> but you might need to extend the databases and/or hack it a bit.  If you 
> really want to do it without even checking the topologies I would prefer 
> a simpler forcefield like Gromos96 over OPLS, though (fewer atom types 
> mean less errors).
> 
> Cheers,
> 
> Erik
> 

I have added this assignment to 
http://wiki.gromacs.org/index.php/Category:Development
it shouldn't be impossible to make this work, but it will require some 
effort.

-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se