Hi >From the following tutorial, the protein pdb file is downloaded from the Protein Data Bank. Before running the MD simulation, we have to make sure the structure property. I have some questions about this tutorials.
http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ 1. Make sure that there are NO Missing residues, missing atoms- http://www.rcsb.org/pdb/files/1lw9.pdb "Search for the presence of REMARK entries with numbers 465 and/or 470. " => there are no REMARK 465 and REMARK 470 ??? 2. The protonation state and side chain orientation of histidine residues may be problematic. => How could I know if they are problematic? => How to do the protonation process on the system? 3. From the tutorial => "Note the numbers of ions added, and verify that an excess of 8 chloride ions is added for neutralization. Having replaced a number of water molecules with ions, the system topology in 1LW9.top is not correct anymore. Edit the topology file and decrease the number of solvent molecules. Also add a line specifying the number of NA+ ions and a line specifying the amount of CL-. " => Would you please explain this more? Thank you very much Lin
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