Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Some SMILE lead to a very large 3D structure (separate each conformer) #10

Open
saurabh2804 opened this issue Nov 10, 2024 · 0 comments

Comments

@saurabh2804
Copy link

saurabh2804 commented Nov 10, 2024

OC(=O)CNC(=O)C1CCCN1 L-Prolylglycine

This formed a multi-conformer sdf "L-Prolylglycine__input2881.sdf" (within the zipped file). Converted it to pdbqt with obabel. I used two flags: -m and -writeconformers
obabel -isdf input.sdf -O drug.pdbqt --writeconformers -m
It wrote a really large 3D PDBQT. Making directly in obabel from SMILE gives a normal molecule.
This is the same for several molecules
Please suggest changes to the process to avoid this issue
L-proglycine.zip

Thank you,
Regards

EDIT: On ubuntu 24.04 and the latest version of Gypsum_DL

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant