Saving multiple conformer into a single file

General Discussion
1

Hi

is there a way to save the multiconformer search into a file?
I mean if I save it, I get only one.

Cheers

2

If you’re referring to Avogadro 1.2, unfortunately no. It’s not actively maintained.

You can, however, use Open Babel (which is used for the conformer searching):
https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#generating-conformers-for-structures

For example:
obabel file.sdf -O conformers.sdf --conformer --nconf 20 --weighted --writeconformers

This will generate 20 conformers from file.sdf into the new file conformers.sdf

3

thanks yes it was 1.2
I was using Unicon for conformer then avogadro 1.2 using MM4 on each of the conformers (in the same mol2 file), then I wanted to save them all as optimized…which I would have use the mol2 file to convert it into xyz.
In order to use ORCA implemented with XTB to optimized again, but probably don’t need to do MM4 then XTB2.
It was just to play with it.

cheers

4

If you’re using XTB, you can also use Crest:

It can generate conformers at the GFN2 (XTB2) level. Maybe a bit slower, but it’s a great tool using either .mol files or .xyz.

You can split the resulting files with obabel too.

(which reminds me, I need to write a crest plugin for Avogadro2)

5

Yes I know, problem setting it up, but I will cheers
and yes for the plugin

6

Any idea how to add

at the end of each structures in Openbabel or notepad
for Orca to read them all and play with it??
cheers

7

I’m not sure I understand. Are you saying that obabel is missing a final newline? For what formats?

8

sorry I was looking to add “>” after each structure which was conformered…for orca and its syntax
I found it
sed -e “/^[0-9]/i>” structures.xyz > mynewfilestructures.xyz