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

[ahmet yıldırım]

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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