Any Software/Server available for Protein and metal ions/ inorganic compound docking study
Yes there are many servers and software for it. For online servers you can consider the patchdock, dockblast, docker etc. and for software ICM is one of the best but you can use flex and gold also.
Thank you Rathore and Kesharwani, I did try PathDock and it works fine.....I am going to use Gromacs for further verification.
Moreover what do you people suggest using one molecule (e.g. CdCl2) as a one subunit or multiple attached molecule and then doing docking/simulation
I am sorry Yodendra, I could not make it clear....I wanted to know that using one molecule of Ligand (CdCl2 in my case) will be good for docking or to replace it with the chain of CdCl2-CdCl2........ as a ligand and then do docking study
when you will change the ligand, parameters will also be changed. The free energy change in case of alone CdCl2 will be different from that of the chain of the same ligand. The reason for this is becoz the side chain interaction in case of CDCl2 chain will be higher then the CdCl2 alone. Please be clear, if you will use CdCl2-chain for your docking, it will be considered as a completely different compound and may not be accommodated in the predefined pocket. I will appreciate if others also comment on this issue.
AutoDock
GRAMM-X : http://vakser.bioinformatics.ku.edu/resources/gramm/grammx
try out Docking on this link
Dear Yogendra nice input, I would request rest of members to comment as well as
I am new in this field , using flexX (leadit-2.1.8) for metal ion and protein docking. There is error INVALID MOLECULE when i import metal.mol2/sdf file of metal ion as a ligand .While when any protein .mol2 file import than no problem. Kindly provide me some ideas to overcome this problem.
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