How can I perform ligand-protein interaction analysis (L-P contact) using Gromacs .gro and .xtc outputs on SID (simulation interaction diagram) panel in Schrödinger Maestro version 2022.4?
After converting the .gro file to .pdb with gmx editconf and my .xtc files to .mae file type using VMD 1.9.3, I uploaded my topology and trajectory files to Maestro. Then when I try to create a .cms file using the model system regeneration panel, "WARNING Rebuilding a model system requires a single, full-system entry in the Workspace." I got the warning. So I created the -out.cms file with system builder and minimization. Because the Maestro 2022.4 SID panel only allows -out.cms format for ligand-protein analysis. But it gives error "Couldn't locate a trajectory directory for given CMS file".
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