search

Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
Other
260 stars 59 forks source link

Ligand Destroyed During Build #339

Closed waskom closed 7 years ago

waskom commented 7 years ago

Hello All,

I have been having an issue during the building process where the ligand gets dissected during the building process. The PDB coordinates look the same as the input structure. I am not sure how to proceed.

Thank you, Mike

screen shot 2017-05-16 at 11 00 57 am
cuzzo87 commented 7 years ago

Hello Mike,

Thank you for the jupyter screenshot, but to help you in this stage I need to ask you more information about your protocol. First I would like to understand at which stage you see the dissected ligand. Is after the building procedure? If it is this the case, based on the screenshot I cannot see the build command. Can you provide me the jupyter you are using? Furthermore could you please give me information regarding the ligand parametrization?

waskom commented 7 years ago

I see the ligand destroyed after the whole system is built. I have uploaded the notebook. The parameters have been from the parachem server.

DAT_MPH_2.ipynb.zip

waskom commented 7 years ago

The ligand is fine when the visualization occurs after the protein, lipid, and ligand are put together.

waskom commented 7 years ago

I figured it out. It was an issue with the parameters.