Hi Mr.Zeeshan,

You can try Avagadro software for ligand preparation and optimization purposes.

You can try the Ligandscout of inteligand (www.inteligand.com).

Hello,

You can try Openbabel for basic manipulations such as spatial representation and minimization. If you need tautomer enumeration you can try with SPORES.

Hope this helps,

Regards

Dear Zafar,

I reproduce here the recommendation already available in Reserach Gate by Mr. Manimaran:

Ligand Optimization Procedure:

1. Convert your ligand MOL2 to PDB format file using OpenBabel software (http://openbabel.org/wiki/Get_Open_Babel)

2. Go to PRODRUG server (http://davapc1.bioch.dundee.ac.uk/prodrg/submit.html) paste your ligand PDB file and submit.

Another site that may be helpfull in case you need topology and parameters for small organic molecules

https://www.swissparam.ch/

Good luck