# [CP2K:6844] Non-integer charge in the classical part of QM/MM system

tarak karmakar tarak... at gmail.com
Sat Aug 1 07:49:36 UTC 2015

```Thanks Teo for the quick reply and suggestion.
What would you recommend for the GLY residue?
Is a cut in the CA-C bond a good choice for GLY?

In my system, I have two consecutive residues CYS 99 and GLY 100 in the
active site which I need to include in the QM part.
Now, what I did as of now is, I cut a bond
i) between N of Ser 98 (previous residue) and CA of CYS 99.
ii) between CA of GLY 100 and C of GLY 100

While I do the above, I have got a non-integer charge of +1.68 for the
classical part.
I calculated the sum of the atomic charges (atoms I selected for the QM
part) and got +0.32.

-----------------------------------------------------------------------------------
2707  99  CYS  CA   CT1    0.070000       12.0110           0
2708  99  CYS  HA   HB1    0.090000        1.0080           0
2709  99  CYS  CB   CT2   -0.110000       12.0110           0
2710  99  CYS  HB1  HA2    0.090000        1.0080           0
2711  99  CYS  HB2  HA2    0.090000        1.0080           0
2712  99  CYS  SG   S     -0.230000       32.0600           0
2713  99  CYS  HG1  HS     0.160000        1.0080           0
2714  99  CYS  C    C      0.510000       12.0110           0
2715  99  CYS  O    O     -0.510000       15.9990           0
------------------------------------------------------------------------------------------Total=
0.16
1043 100  GLY  CA   CT2   -0.020000       12.0110           0
1044 100  GLY  HA1  HB2    0.090000        1.0080           0
1045 100  GLY  HA2  HB2    0.090000        1.0080           0
1046 100  GLY  C    C      0.510000       12.0110           0
1047 100  GLY  O    O     -0.510000       15.9990           0
-----------------------------------------------------------------------------------
Total = 0.16

The total charge in the QM part is -2.

So, I will get an excess charge of +0.32 (or opposite, -0.32) from the
atoms described in the QM part, right?
Distribute this excess charge in the MM part, does that mean I need to
adjust the charges of the MM atoms in the .psf file to make my system
neutral?

Thanks,
Tarak

On Sat, Aug 1, 2015 at 12:35 PM, Teodoro Laino <teodor... at gmail.com>
wrote:

> 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>
> 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
>>
>>  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
>>      BASIS_SET_FILE_NAME  ./GTH_BASIS_SETS
>>      POTENTIAL_FILE_NAME  ./GTH_POTENTIALS
>>
>> 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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