[gmx-users] charge groups

Eric Jakobsson jake at ncsa.uiuc.edu
Sat Apr 17 21:04:00 CEST 2004

We first tackled that in our first membrane simulation paper in '95, 
because we did ab initio calculation of charges in phospholipid head groups 
and then wanted to create neutral charge groups.  We were able to do this 
with adjustments of no more than .2 electron charges on any atom from the 
calculated charges.  We deemed this to be an acceptable adjustment, 
especially given the conceptual crudity of translating the QM calculation 
into partial charges on psuedo-classical atoms.


At 12:44 PM 4/16/2004 +0300, you wrote:
>I'm fluding gmx community with question of different kind concerning
>new topoly creation. I got one more about charge groups.
>I'm introducing one extra oxygen atom in heme topology, i.e.
>ff43a1.rtp file. I made ab intio calculation of new oxidation state of
>heme recidue with bound oxygen to Fe. I got charges which I want to
>introduce to heme atoms instead of old ones. After I analysed old heme
>charges I realised that it has -2 of total charges. Carbon atoms of
>pyrole groups in heme have charge 0 !
>However, my ab intio network of charges is very different.
>What king of "make-up" rules should be applicated to my QM charges in
>order to "distribute" charges right according charge group concept ?
>With best wishes
>dr. A.Ziemys
>gmx-users mailing list
>gmx-users at gromacs.org
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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