<br>Hi <br>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.<br>
<br><a href="http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/">http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/</a><br><br>1. Make sure that there are NO Missing residues, missing atoms-<br> <a href="http://www.rcsb.org/pdb/files/1lw9.pdb">http://www.rcsb.org/pdb/files/1lw9.pdb</a><br>
"Search
for the presence of REMARK entries with numbers 465 and/or 470.
" => there are no REMARK 465 and REMARK 470 ???<br><br><br>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?<br><br><br>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-.
" <br> => Would you please explain this more?<br><br>Thank you very much<br><br>Lin<br><br><br><br><br>