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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 31 08:43:28 CEST 2011


Hi Ahmet,

As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have zero charge,
nor integer charge. In your case, I'd suggest two COH groups for EDO,
which will have zero net charge each, and for TRS I'd take the COH
groups as separate charge groups. I also note that the COH groups,
although chemically identical - H3NC(COH)3, right?-, have different
charges. That doesn't seem proper.

Hope it helps,

Tsjerk

2011/3/31 ahmet yıldırım <ahmedo047 at gmail.com>:
> 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
>
> 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.
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands


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