I want to convert a SMILES code into a 3D SDF and PDB files to use for docking.I am using the following module:
http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
The first CONVERSION step seems OK where I either draw the compound in the window or paste SMILES code into the sketcher.
In the middle window, I choose Input file as "SMILES" and out file as "SDF".Then I choose 3D and add hydrogens.Then I click CONVERT. I get a code in the OUTPUT window. Here I am stuck.
How I export the file as SDF and save it? The tool does not allow me a file path.
Babel documents dont help.
Thanks
Copy and and paste that output into a text file. Then change the file name extension of that text file from .txt to .sdf. In a linux system changing the filename extension is easy but in widows system it maybe a bit tricky; first in the folder option you have to check the show extension for known file types option.
I am unable to understand why a simple SAVE process is made so complicated. I have no experience of linux
Thanks Qazi sahib. Which tool you recommend to convert pdf to sdf format?
Babel ?
Thanks Qazi sahib,
cactus is working and is very simple and straightforward to use.
- Badges
- Science topic
- Similar topics
- Filing