[gmx-users] the total charge of system is not an integer

[Mark Abraham]

On 31/03/2011 5:18 PM, ahmet y?ld?r?m wrote:
> Dear users,
>
> Before energy minimization step , I performed the preprosessing step 
> using grompp .
> However, there are two note that :
>
> *_NOTE 1 [file topol.top, line 52]:_*
>   System has non-zero total charge: -1.500000e+01

This is an integer. See 
http://en.wikipedia.org/wiki/Scientific_notation#E_notation and 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

> _*NOTE 2 [file topol.top]:*_
>   The largest charge group contains 11 atoms.
>   Since atoms only see each other when the centers of geometry of the 
> charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

See Tsjerk's email.

Mark

> *
> PS: *TRS and EDO are not aminoacid*
>
> _TRS.itp:_*
> ..
> [ moleculetype ]
> ; Name nrexcl
> TRS      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1        OA     1  TRS      O1     1   -0.119  15.9994
>      2         H     1  TRS     H13     1    0.032   1.0080
>      3       CH2     1  TRS      C1     1    0.087  14.0270
>      4      CCl4     1  TRS       C     2    0.055  12.0110
>      5       CH2     1  TRS      C3     2    0.049  14.0270
>      6        OA     1  TRS      O3     2   -0.205  15.9994
>      7         H     1  TRS     H33     2    0.019   1.0080
>      8        NL     1  TRS       N     2    0.206  14.0067
>      9         H     1  TRS      H2     2    0.004   1.0080
>     10         H     1  TRS      H3     2    0.004   1.0080
>     11         H     1  TRS      H1     2    0.004   1.0080
>     12       CH2     1  TRS      C2     2    0.050  14.0270
>     13        OA     1  TRS      O2     2   -0.205  15.9994
>     14         H     1  TRS     H23     2    0.019   1.0080
> ...
>
> _*EDO.itp*_
> ...
> [ moleculetype ]
> ; Name nrexcl
> EDO      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1        OA     1  EDO     OAB     1   -0.111  15.9994
>      2         H     1  EDO     HAE     1    0.031   1.0080
>      3       CH2     1  EDO     CAA     1    0.080  14.0270
>      4       CH2     1  EDO     CAC     1    0.080  14.0270
>      5        OA     1  EDO     OAD     1   -0.111  15.9994
>      6         H     1  EDO     HAF     1    0.031   1.0080
> ...
> _*
> topol.top:*_
> ..
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
> #include "TRS.itp"
> #include "EDO.itp"
> ..
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> SOL               185
> SOL               143
> TRS                1
> EDO                1
> SOL             44125
> *_
> Conf.gro:_*
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>  5354
>     2GLN      N    1   1.458  -1.158   0.739
>     2GLN     H1    2   1.520  -1.083   0.763
> .......
>   485HOH    HW1 5333   0.221  -3.864  -2.291
>   485HOH    HW2 5334   0.303  -3.946  -2.407
>     1TRS  O1       1  -3.812  -0.471  -2.002
>     1TRS  H13      2  -3.865  -0.443  -1.922
>     1TRS  C1       3  -3.672  -0.469  -1.971
>     1TRS  C        4  -3.635  -0.571  -1.863
>     1TRS  C3       5  -3.711  -0.547  -1.731
>     1TRS  O3       6  -3.694  -0.414  -1.679
>     1TRS  H33      7  -3.746  -0.404  -1.594
>     1TRS  N        8  -3.673  -0.705  -1.911
>     1TRS  H2       9  -3.625  -0.725  -1.996
>     1TRS  H3      10  -3.771  -0.707  -1.927
>     1TRS  H1      11  -3.649  -0.774  -1.842
>     1TRS  C2      12  -3.483  -0.573  -1.840
>     1TRS  O2      13  -3.428  -0.445  -1.806
>     1TRS  H23     14  -3.470  -0.412  -1.722
>     1EDO  OAB      1   0.307  -2.792   0.149
>     1EDO  HAE      2   0.390  -2.826   0.104
>     1EDO  CAA      3   0.239  -2.901   0.212
>     1EDO  CAC      4   0.111  -2.851   0.281
>     1EDO  OAD      5   0.144  -2.763   0.388
>     1EDO  HAF      6   0.060  -2.731   0.432
>    8.13100   7.04165  13.54850   0.00000   0.00000  -4.06550   
> 0.00000   0.00000   0.00000
>
> How can I fixed these notes(note 1 and note 2)?
>
> Thanks in advance
> -- 
> Ahmet YILDIRIM

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