Error in converting cms file of a ligand with pseudoatom

shirtsgroup / InterMol

Conversion tool for molecular simulations

MIT License

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Error in converting cms file of a ligand with pseudoatom #374

Open amrhamedp opened 3 years ago

amrhamedp commented 3 years ago

Hello, I am trying to convert ligand with pseudo-atom from cms to gromacs. It gives error related to indexing. Hope you resolve this issue

I would appreciate that. Thanks

desmond_setup_2-out.cms.zip

amrhamedp commented 3 years ago

I can work on it but I need advice: 1-It seems that file has mixed 1-4 scaling....not sure how intermol handles this for gromacs conversion 2-Dr shirts seems to have a branch for intermol "virtualgd" but it doesn't handle conversion of virtuals from desmond to gromacs....it seems it is working on the reverse direction but not from desmond.

amrhamedp commented 3 years ago

@mrshirts can anyone please reply to me?

mrshirts commented 3 years ago

I apologize in the delay for answering. Unfortunately, I don't know that we have the staffing to resolve this issue right now. Some work going on for improvements, but it will likely be a few months.