Thanks Goette for your mail. So system neutrality is restored as per your advice but individual residue will deviate from its integer value (formal charge), wonÂ’t violate anything? I remember once I read the lines of individual residues' partial charge should be an integer from gromacs manual, I really took some time to search it in manual to refer that line in this mail, but I could not find it. But I am also using Autodock (Docking tool), where the non-integral charge on residue based is not allowed. May be I overlapped these two programs concept of partial charges!
By, B.Nataraj the desired partial charge On Tue, 28 Nov 2006 11:48:40 +0100, "Maik Goette" <[EMAIL PROTECTED]> said: > Hi > > Depends on your system, but in principle yes. > A Cystein should be neutral. If you take a deprotonated one to build a > complex with the zinc, it should be neutral afterwards. > > Lets assume a case with HIS/HIS/CYS as complex partners. the resdiues > without a complex are assumed to be neutral. Therefore, their charges > added should be 0. Add your zinc to the complex, take a partial charge > of 0.7xx for it and modify the charges of the complex partners (i.e. the > S and in the case of histidine it makes sense to spread the charge > difference over the ring). If you now add up all the charges of all > complex partners, the system should again be at charge 0. > I can't see the problems, sorry. > > Regards > > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > raja wrote: > > Dear Mark, > > Thanks for your reply. Well, I have well taken your point of making > > separate charge group constituting Zn and its residues and I am working > > out for it, in mean time I need some clarification in my present > > approach. > > > > I just detailed out my earlier mail hereunder. I am using AMBER force > > field. > > > > This is default partial charge distribution for deprotonated Cystine > > CYM N -0.4157 > > CYM H 0.2719 > > CYM CA -0.0351 > > CYM HA 0.0508 > > CYM CB -0.2413 > > CYM HB1 0.1122 > > CYM HB2 0.1122 > > CYM SG -0.8844 > > CYM C 0.5973 > > CYM O -0.5679 > > ------------------------ > > Formal Charge = -1.00000 > > ---------------------------- > > > > Now my modified partial charge at SG to -0.6944 > > > > CYM N -0.4157 > > CYM H 0.2719 > > CYM CA -0.0351 > > CYM HA 0.0508 > > CYM CB -0.2413 > > CYM HB1 0.1122 > > CYM HB2 0.1122 > > CYM SG -0.6944 > > CYM C 0.5973 > > CYM O -0.5679 > > ------------------------ > > Formal Charge = -0.8100 > > ----------------------- > > > > According to manual, to ensure integer value of total charge on the > > residue CYM (cysteine). Ideally, following the force field convention, I > > would like to do readjustment of the individual partial charges to make > > it as total = -1. But on other hand this is my intuition that, formal > > charge for -1 for CYM is applicable for free Cysteine residue in AMBER > > force field, but in my case, it is harmonically bonded with zinc and > > also the charge transfer is taken place. This makes me to think that the > > formal charge of CYM should be adjusted to neutral. Please give your > > thought? > > > > With thanks ! > > B.Nataraj > > > > > > > > > > > > > > > > > > > > > > > > On Tue, 28 Nov 2006 17:51:04 +1100, "Mark Abraham" > > <[EMAIL PROTECTED]> said: > >> raja wrote: > >>> Hi gmxions, > >>> There are many references, say that Zn2+ partial charge should be > >>> reduced to ~0.7 rather than the force field default value of 2. In line > >>> with that there are many values published for distributed charge in its > >>> surrounding ligand atoms in compensation for loss of positive charge of > >>> Zn. > >> OK, so this strategy preserves charge neutrality over the zinc and a > >> bunch of ligand residues. It will not preserve charge neutrality of the > >> individual residues, obviously. > >> > >>> Now I am having set of values to be distributed for my system's > >>> active site residues, say for one SG-Cys, and two NE2-His atoms. My > >>> question is that what will be net formal charge for these residues after > >>> its specific atoms' charges are modified. > >> The old value, plus the modification? > >> > >>> In other words, for example, > >>> after modifying default partial charge of SG-Cys from -0.8844 to > >>> -0.6944, Should I adjust its net formal charge to -1 or to 0? > >> Not sure where you're adjusting the "net formal charge" or why you think > >> it's necessary. > >> > >> What you really want to do is have charge groups with integral values of > >> charge (see section 3.4.2 and some part of Chapter 5 for how to do > >> this), so that probably means combining the zinc with chunks of these > >> residues into one large +2 charge group. > >> > >>> Then on > >>> what basis I can adjust rest of the atoms’ partial charges. > >> Why would you do this? Whatever you do should be consistent with the > >> most reliable scheme in the literature, unless you want to create an > >> expensive random number generator. > >> > >> 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 > _______________________________________________ > 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 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Same, same, but differentÂ… _______________________________________________ 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
