I am using Autodock4 for protein-ligand interaction. I need a pdb or mol2 file for ligand. I have downloaded sdf file and convert it in pdb and mol2 file by using save as option. But these files are not working in autodock. For visualization I am using PyMol but i am not seeing any structure in that also. Can someone please help ..
Hello, I recommend openbabel but be very careful, if in the future you need to maintain an organization when it comes to the atoms label I recommend using another application. This problem makes it difficult for some programs to calculate RMDS.
Example:
current_file
-----------------------
...
... C1
... H1
... N2
conversion_babel
-----------------------
...
... C
... H
... N
Use the following web-page to easily convert between different file format, especially mol2 format. I had great difficulty converting my ligand file to mol2. Finally found this website. Even I tried "Openbabel" recommended by many without any success. With this web-page, you don't even need to install anything.
http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
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