cmb411 at psu.edu
Fri Oct 24 20:08:01 CEST 2003
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!
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