4/6/2024 0 Comments Maestro schrodingerThe capability to search for interactions between protein and ligands, incuding Hydrogen bonds, Pi-Pi interactions (face to face, face to edge), Halogen bonds, Salt bridges and Metal-ligand/protein bonds.RCSB metadata (deposition date, resolution, etc.).Density data: fo-fc and 2fo-fc electron density maps.The PLDB is a fully annotated and curated version of the PDB that you can use to run querys against. The Protein Ligand Database (PLDB) is part of the Schrödinger Suite available at Stanford. Note: the -X option enables Maestro graphical GUI access. Those should be submitted to the scheduler which will dispatch them on compute nodes. Note: Login nodes are usually shared among many users and therefore must not be used to run computationally intensive tasks. You can request more resources for interactive jobs by following these instructions. For more intensive jobs such as MD you will need to use SLURM to submit your job (see article above). Note: The " sdev" command is intended for quick jobs and will allocate one core and 4 GB of memory on one node for one hour. Also note, the standard scripts detailed in the Schrodinger Script Center (see above) are already installed for you so there is not need to download. Note: $SCHRODINGER is the environment variable already setup for you, this parameter loads all the paths to find the software. Step 4 - Load the 'chemistry' meta-module and then the 'schrodinger' module:
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