[gmx-users] the reson for neutralizing the charge

[hazizian]

Hi
my ligand is Arginine (so it is not neccessary to use PRODRG )and the OPLS 
forcefield of gromacs make the itp file of it. I check and all the atoms 
present in the ligand itp file.There is no missing atom in the file.

 atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    
chargeB      massB
     1   opls_287      1    ARG      N      1       -0.3    14.0067   ; qtot 
-0.3
     2   opls_290      1    ARG     H1      1       0.33      1.008   ; qtot 
0.03
     3   opls_290      1    ARG     H2      1       0.33      1.008   ; qtot 
0.36
     4   opls_290      1    ARG     H3      1       0.33      1.008   ; qtot 
0.69
     5   opls_283      1    ARG     CA      1       0.04     12.011   ; qtot 
0.73
     6   opls_140      1    ARG     HA      1       0.06      1.008   ; qtot 
0.79
     7   opls_136      1    ARG     CB      2      -0.12     12.011   ; qtot 
0.67
     8   opls_140      1    ARG    HB1      2       0.06      1.008   ; qtot 
0.73
     9   opls_140      1    ARG    HB2      2       0.06      1.008   ; qtot 
0.79
    10   opls_308      1    ARG     CG      3      -0.05     12.011   ; qtot 
0.74
    11   opls_140      1    ARG    HG1      3       0.06      1.008   ; qtot 
0.8
    12   opls_140      1    ARG    HG2      3       0.06      1.008   ; qtot 
0.86
    13   opls_307      1    ARG     CD      4       0.19     12.011   ; qtot 
1.05
    14   opls_140      1    ARG    HD1      4       0.06      1.008   ; qtot 
1.11
    15   opls_140      1    ARG    HD2      4       0.06      1.008   ; qtot 
1.17
    16   opls_303      1    ARG     NE      5       -0.7    14.0067   ; qtot 
0.47
    17   opls_304      1    ARG     HE      5       0.44      1.008   ; qtot 
0.91
    18   opls_302      1    ARG     CZ      5       0.64     12.011   ; qtot 
1.55
    19   opls_300      1    ARG    NH1      6       -0.8    14.0067   ; qtot 
0.75
    20   opls_301      1    ARG   HH11      6       0.46      1.008   ; qtot 
1.21
    21   opls_301      1    ARG   HH12      6       0.46     1.008   ; qtot 
1.67
    22   opls_300      1    ARG    NH2      7       -0.8    14.0067   ; qtot 
0.87
    23   opls_301      1    ARG   HH21      7       0.46      1.008   ; qtot 
1.33
    24   opls_301      1    ARG   HH22      7       0.46      1.008   ; qtot 
1.79
    25   opls_271      1    ARG      C      8        0.7     12.011   ; qtot 
2.49
    26   opls_272      1    ARG     O1      8       -0.8    15.9994   ; qtot 
1.69
    27   opls_272      1    ARG     O2      8       -0.8    15.9994   ; qtot 
0.89

So for neutralizing I break 0.11 charge to 8 number of 0.01 charge and 6 
number of 0.005 cherge and add them to 8+3=11 H atoms. so the total charge 
of my ligand is +1.Is it correct way to solve this problem in the case that 
I could not find any missing atom in ligand topology file?


Tehran University of Medical Sciences
www.tums.ac.ir


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