Ligands discarded


I am facing an error with the structure I’ve uploaded. Despite uploading .lib and .frcmod files, my ligand is getting discarded.
I have a phosphotyrosine in my structure, and as recommended for AMBER full MD setup, I changed ATOM to HETATM for it. I also changed other parameters as per AMBER (OG to OS etc.). After these changes, my ligand Y1P for phosphotyrosine is still discarded.

I am very new to MD so I may be missing out on something. Please guide me.



for what you are explaining, you are following all the steps required for this particular process. I would like to help you solve your issue, but I will need more information, such as your MDWeb user id. Please contact me directly in this e-mail address: and we can open a private conversation.

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