# Ligands discarded

**URL:** <https://ask.bioexcel.eu/t/ligands-discarded/2303>\
**Category:** MDWeb\
**Created:** [July 4, 2020, 10:30am UTC](https://ask.bioexcel.eu/t/ligands-discarded/2303 "2020-07-04T10:30:33Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![help\_me](https://avatars.discourse-cdn.com/v4/letter/h/958977/32.png) [@help\_me](https://ask.bioexcel.eu/u/help_me)\
**Post date:** [July 4, 2020, 10:30am UTC](https://ask.bioexcel.eu/t/ligands-discarded/2303/1 "2020-07-04T10:30:33Z")

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Hi

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.

Thanks

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**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\
**Post date:** [July 9, 2020, 12:10pm UTC](https://ask.bioexcel.eu/t/ligands-discarded/2303/2 "2020-07-09T12:10:23Z")

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Hi,

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: [adam.hospital@irbbarcelona.org](mailto:adam.hospital@irbbarcelona.org) and we can open a private conversation.

Thanks for using our tools!

Regards,

-Adam-