Is it possible for you to provide the processed cocrystal pdb right before md simulation?

t7morgen / misato-dataset

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Is it possible for you to provide the processed cocrystal pdb right before md simulation? #11

Closed YangChemE closed 5 months ago

YangChemE commented 5 months ago

Hi, We are trying to use the MD dataset for some analysis, however the naming and arrangement of atom names and indices (especially for the ligand) are not really comparable to the original pdb file, and creating a mapping doesn't seem easy. Is it possible for you to provide the original file (i.e. the one with the cocrystal coordinates but your way of naming) before the simulaition?

Thanks!

t7morgen commented 5 months ago

Hi, did you have a look at the restart and parameter files in AMBER format? It can be downloaded from zenodo in the file called: parameter_restart_files_MD.tar.gz. These files can be opened and viewed with common visualization programs (e.g. VMD) and the coordinates match the last frame in the MD.hdf5. We will try to upload the starting files with the next release.