i am doing Md-smulation of protein-ligand complex by using NAMD and VMD but my Lig.str file is not generating from .mol2 file from CGenFF. i don't know why . it shows error of non-unique atom . can anyone help me to findout this error. i have attached my.mol2 file here.or guide me about another software through which Lig.str can made?
You can use the Swiss Param http://www.swissparam.ch/ server for ligand str file generation
MY Mol2 file is not generating LIG.str file . i have attached mol2 file with it Piyush Kumar Yadav . kindly tell me the reason if you understand.
It's not online but there are some different options to receive ligand topology files. Moreover, do you really need a CHARMM ff? If you could use AMBER, try openFF.
I'm not pretty sure but parmed (https://parmed.github.io/ParmEd/html/index.html) has such functionality. There are pyCHARMM (https://github.com/BrooksResearchGroup-UM/pyCHARMM-Workshop) for CHARMM, CHAMM-GUI (https://charmm-gui.org) and some CHARMM scripts (https://github.com/Birdlet/Charmm2Slipids).
I do hope you will find it useful!
Dear Ariha Zaid I have generated your LIG.str file using the http://www.swissparam.ch/ you can also explore the tool
Ariha Zaid your ligand files are not prepared, so I will suggest you to please prepare your mol2 files and then upload in swiss PARAM server