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

tarak karmakar tarak... at gmail.com
Sat Aug 1 09:42:04 UTC 2015

```>From a QM/MM tutorial in amber,
http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-qm-mm/qm-min.out
I have got the following,

Sum of charges from parm topology file =  -1.00010025
QMMM: ----------------------------------------------------------------------
QMMM: Uniformally adjusting the charge of MM atoms to conserve total charge.
QMMM:                             qm_charge =   -1
QMMM: QM atom RESP charge sum (inc MM link) =   -0.590
QMMM: Adjusting each MM atom resp charge by =    0.000
QMMM:          Sum of MM + QM region is now =    0.000
QMMM: ----------------------------------------------------------------------

The charge has been adjusted automatically in the MM atoms.

Does CP2K has this kind of procedure?

Thanks,
Tarak

On Sat, Aug 1, 2015 at 1:19 PM, tarak karmakar <tarak... at gmail.com> wrote:

> 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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>
>
>
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