> Dear All who may concern, > I have some questions for the charge calculation in Gromacs, I used > the > forcefied ffG43a1 for the protein and inhibitors. Does the charge for the > protein is the charge per residue?
The charge on a residue is the sum of the charges on the (united) atoms that make it up. The charge on a protein is the sum of the charges on the residues that make it up (or all of the atoms, obviously). The charge per residue is almost never considered, as it normally doesn't aid anybody understanding physical behaviour. Hope that answers your question, because I can't understand it. > This forcefield is just for the polar > H, > right? For the nonpolar H, it will merge the H into the Heavy atom, right? Don't know in this specific case, but there are such forcefields. > I > would like to know that does this force field also calculate the charge > for > the nonpolar H and then sum the charge with the heavy atom which it > connects > to or it doesn't calculate the charge for the nonpolar H? The charge on a united atom is just a number - as is the charge on a polar H, or any H in a non-united-atom force field. You can think of it as the sum of the charges on the multiple atoms it models if it helps. > Does the charge > of > the Heavy atom is its own charge without sum together with the nonpolar H > which connect to it? Moreover, I would like to know that if I would like > to > use quantum mechanics (qm) to calculate the charge for my inhibitor, what > should be the method and the basis set to use to calculate for the charge > to > make it compiles with the ffG43a1 force fields? Sounds like you should find the documentation (journal article?) for this force field and read it. Also some introductory material on how force fields work sounds like it might be worthwhile :-) Wanting to extend a force field you don't understand yet is a recipe for disaster... Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
