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 [email protected] > 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 - Faster than the air-speed velocity of an unladen european swallow _______________________________________________ gmx-users mailing list [email protected] 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
