You can try using Swiss pdb viewer. They have nice tutorial for protein modelling and is easy to use.

Let me know if you need more help. 

Thanks. Vrushali,  how to use swiss pdb viewer if i model my sequence using Swiss-model? 

Thanks, Ashish, How to link new-modelled protein with protein loop modelling server?

@BM

If you are new to some technique, firstly, please do read literature and try to use some basic available tools.

For steps please see this paper :

https://www.researchgate.net/publication/216432591_Prediction_of_Medicinal_Properties_of_Marine_Biota_using_Computational_Bioinformatics_Techniques

One stop resource for your work:               www.click2drug.org

Must visit this link on  insilico s/w tools 

https://www.researchgate.net/post/Has_any_one_compiled_a_list_of_software_processes_used_in_the_CADD

Please do not hesitate for any help you need 

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