jake at ncsa.uiuc.edu
Fri Oct 24 23:59:00 CEST 2003
Almost everybody does what you point out we should not do, and keeps the
same atomic charges throughout the calculation. That is why we sometimes
do not get such great results in simulations where ions interact with
Anybody who can fix that with reasonable computational efficiency, would be
doing a great thing.
At 02:07 PM 10/24/2003 -0400, you wrote:
>It seems to me that the only place where charges are specified for atoms in a
>molecule is ff???.rtp file. Well, I have a molecule which is not a protein and
>for which I write the topology myself. I skip the step of using the pdb2gmx
>program in order to create a *.top file automatically. I guess I have to
>specify charges of the atoms in the molecule in a column next to that one with
>masses in the *.top(or *.itp)file ....
>So, I do not know where from to take the charges for the atom types I need for
>my molecule. I've seen some 0s in the ffG43a2nb.itp file. Plus, their sum
>should be 0(if I consider cgnr = 1 for all of them).
>What's the general procedure, how people deal with charges? For a
>instant I can take them from a ab initio calculation, but my molecule
>conformational changes over time and these charges should change...plus I have
>to apply electric field which makes them change even more. Is that enough for
>the ff if I provide a set of initial partial charges from ab initio calc?
>Somebody sure knows the answer! Thaks very much in advance!
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
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
(Currently on leave to NIH to serve as Director of Center for
Bioinformatics and Computational Biology at the National Institute of
General Medical Sciences and Chair of the NIH Biomedical Information
Science and Technology Initiative Consortium. Usual schedule is four days
a week at NIH and three days a week at Illlinois.)
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