Non-integer charge in the classical part of QM/MM system

tarak karmakar tarak... at
Sat Aug 1 06:16:23 UTC 2015

I think I have got the clue to the charge related issue.
First thing I missed is one oxygen with a charge of -0.51.
Now, the total charge in my classical system is +1.68.
I checked in literature and found out that Gly, Ala, and Pro residues can
not be cut up to CA, rather one should select the entire residue by using a
backbone cut. In my system, there are two Gly residues that I selected up
to the CA atom. If I add the N and HN of these residues the total classical
charge is coming out to be +2.00.


On Fri, Jul 31, 2015 at 10:04 PM, tarak karmakar <tarak... at>

> Dear All,
> I am trying to study an enzymatic reaction of an enzyme using CP2K. While
> running the QM/MM simulation I notice the following,
>  CHARGE_INFO| Total Charge of the Classical System:
> 1.170000
>  DFT|
> Charge                                                                  -2
> From an old post
>  I realize that the user should take care of the non-integer charge, if it
> is there.
> In my system, the reaction substrates in the active site have a total -2
> charge while the surrounding amino acids are all neutral. Thus in the DFT
> section I have mentioned the following,
> &DFT
>      CHARGE -2
> I have checked my .psf file, and the sum of all the atomic charges of the
> system is zero.
> So, my query is whether the partial charge arises due to the inappropriate
> selection of amino acid fragments in the QM region?
> I would appreciate if someone could help me in this issue.
> Thanks,
> Tarak
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