Vmd movie maker11/30/2023 ![]() ![]() Select the protein chain by typing chain X where X is the chain single letter code. Now you can map back the position of the ligand such that said mirror image of the protein sits at the center of the box.Ĭreate an index file for the protein using make_ndx: In the original data, the ligand would usually diffuse around and interact with different mirror images of the protein. Further assume that you want to center the protein in the simulation box. Assume, that you work with a small ligand and a larger binding partner (the protein). To remove periodicity of the trajectories, you need a few tricks. A good choice is the PDB you obtain after setting the box dimensions for your system. So always keep a PDB for your current topology. Working with PDBs that contain two chainsĬhain names are not supported in. Trjconv -b FIRST_TIME_STEP -e LAST_TIME_STEP -f INPUT.xtc -o OUTPUT.xtc Then chose File > Save coordinates.Įxample: remove all hydrogens from a PDB. savepdb "MOVED.pdb"Īlternative: use key '7' and move molecule with the mouse pointer.
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