Re: [Open Babel] obminimize

[<chr...@bt...>]

Great after a few attempts I see what my problem was:-

If I try the sort of construction used for other babel commands

ChrisMacbookPro:~ swain$ /usr/local/bin/obminimize -ff -ff Ghemical -cg -n 2500 -c 1.0E-5 -cut -rvdw6.0 -rele 10.0 -pf 10 '/Users/swain/Desktop/output.sdf' -osdf  '/Users/swain/Desktop/obmin2'
/usr/local/bin/obminimize: cannot read input/output format!
ChrisMacbookPro:~ swain$ 

or

ChrisMacbookPro:~ swain$ /usr/local/bin/obminimize -ff -ff Ghemical -cg -n 2500 -c 1.0E-5 -cut -rvdw6.0 -rele 10.0 -pf 10 -isdf '/Users/swain/Desktop/output.sdf' -osdf  '/Users/swain/Desktop/obmin2'

No file is written


But using

ChrisMacbookPro:~ swain$ /usr/local/bin/obminimize -ff -ff Ghemical -cg -n 2500 -c 1.0E-5 -cut -rvdw6.0 -rele 10.0 -pf 10 -osdf '/Users/swain/Desktop/output.sdf' >  '/Users/swain/Desktop/obmin2'


It works!!

Thanks

Chris




On 18 Feb 2011, at 16:48, Geoffrey Hutchison wrote:

> 
> On Feb 18, 2011, at 11:43 AM, chr...@bt... wrote:
> 
>> Is it possible to get the obminimize tool to output anything other than pdb file format?
> 
> Yes. Supply a '-o[ext]' flag. This works with v2.2 or later. Come to think of it, *you* asked for the feature! :-)
> 
> Cheers,
> -Geoff