Hi Lin, It sounds like you need to look at a basic chemistry or biochemistry textbook. The protein itself in the PDB shouldn't carry a charge explicitly until you decide on the pH of your system and assign the protonation/deprotonation state of residues and add hydrogen atoms appropriately. While their may be ions in a PDB, most of the time you have to add them to ensure neutrality for a simulation with Periodic boundary conditions using PME. I'm not sure what you mean by 'intrinsic counter ions', but generally people use NaCl or KCl.
Josh > Hi > I got the protein crystal structures from the PDB file. > There are only residues and water in the PDB files. > > Why does the protein carry charges? > Why aren't they electrically neutral? > > What are their intrinsic counter ions ? > > Thank you > Lin > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
