[CP2K:6843] Non-integer charge in the classical part of QM/MM system

Teodoro Laino teodor... at gmail.com
Sat Aug 1 07:05:52 UTC 2015

Be careful at the region where you are cutting the aminoacid. Cutting at the amide bond can be tricky because of the highly polarised bond.
Better to cut between CA and CB, i.e. cut a bond that is not highly polarised.

Regarding the charge, you’ll get an excess charge that correspond to the opposite of the sum of the classical charges of your QM atoms.
You can just modify your FF file to distribute the corresponding excess charge to the whole MM system.

> On 01 Aug 2015, at 08:16, tarak karmakar <tarak... at gmail.com> wrote:
> 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. 
> Regards,
> Tarak
> On Fri, Jul 31, 2015 at 10:04 PM, tarak karmakar <tarak... at gmail.com <mailto:tarak... at gmail.com>> wrote:
> 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
> https://groups.google.com/forum/#!searchin/cp2k/charge$20QM$2FMM/cp2k/1BGZ2N3fSKc/J9E5HjI1o4cJ <https://groups.google.com/forum/#!searchin/cp2k/charge$20QM$2FMM/cp2k/1BGZ2N3fSKc/J9E5HjI1o4cJ>
>  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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