How stupid I am! Thanks Fredrik, that fix the problem.
So thanks anyone for helping me.
alchemist
-------- Оригинално писмо --------
От: Fredrik Wallner fred...@wallner.nu
Относно: Re: [Open Babel] obminimize
До: Оги Боги
Изпратено на: Четвъртък, 2013, Февруари 28 14:59:46 EET
Hi,
You should have two dashes before ff, that is
obabel orig.sdf -O
result.sdf --minimize --sd --ff MMFF94
/Fredrik
28 feb 2013 kl. 13:25 skrev Оги Боги <
alchemist...@abv.bg >:
Thank you, Chris
It seems that it works fine now. But I would like to change force field. Ho to
do that? I tried
obabel orig.sdf -O
result.sdf --minimize --sd -ff MMFF94
but openbabel says:
Cannot read input format "" for file "MMFF94"
Could anyone tell me how to change force field?
alchemist
-------- Оригинално писмо --------
От: Chris Morley
c.mor...@gaseq.co.uk
Относно: Re: [Open Babel] obminimize
До:
openbabel-discuss@lists.sourceforge.net
Изпратено на: Четвъртък, 2013, Февруари 28 12:07:12 EET
On 28/02/2013 07:48, Оги Боги wrote:
> Thank you guys for your answer. I tried what you said but the output is
> not a sdf file. How to format it in order to obtain normal sdf file?
An alternative way of accessing the same functionality is to use the
--minimize op with obabel, which provides more flexibility in the input
and output. So, for instance,
obabel orig.sdf -O result.sdf --minimize -f1 -l2
will optimize the first two molecules in orig.sdf and output to
result.sdf. Type obabel -L minimize for more details.
Chris
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