I would like to add metal ion to specific amino acid of predicted protein structure which is in pdb format. VMD looks really hard to play with, so are there any other software which has user friendly interface to do that?
Thank you
You might try this server: Metal Ion-Binding Site Prediction and Docking Server
MIB: http://bioinfo.cmu.edu.tw/MIB/
Dr Thirumal Kumar D , Thank you for the reply, I want docking only not prediction. I already have that information. I want more information on chain format.
Hi Vikram,
As mentioned earlier, I have information about those amino acid, so i know which and where to insert metal ion. It would be great help if you recommend me user friendly interface where minimal codes work. I am no good in writing codes.
Thank you.
Hi Sandeep,
You can rather use Packmol to prepare your initial configuration
Visit the following link for more details.
http://m3g.iqm.unicamp.br/packmol/home.shtml
Hey guys,
Thank you for the suggestion. Autodock is not working on my windows 10. any suggestions to install it?
It get installed but when i try to run, program does not respond at all.
Hi SAMEE ULLAH,
I was able to add metal, but I am not able to move it. Also, how can I make it look bigger? Is it possible to bond with a specific amino acid?
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