spoel at xray.bmc.uu.se
Fri Oct 24 21:40:01 CEST 2003
On Fri, 2003-10-24 at 20:07, CORINA BARBU 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 undergoes
> 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!
start by using the prodrg server to create topology and then you could
do ab initio but you're basically on your own out there...
Do also check the archives for this topic.
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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