[gmx-users] non-integral charge on my modeled protein structure

[sonali dhindwal]

Hello Everyone,
I have a same query, I asked before, but couldnt get a solution for that,
I have one modelled protein strucutre,,and when I run pdb2gmx to generate topolgy file, it gives charge in non-integral value. In terminal then it gives warning of protein having non-integral charge. Moreover, in the toplogy file qtot for the last residue comes out to be different than that is shown in terminal as warning.
I am pasting some part of end of my topology file's [atom] part here.
  4883        CH1    493    LEU     CG   2100          0     13.019   ; qtot -1.94
  4884        CH3    493    LEU    CD1   2100          0     15.035   ; qtot -1.94
  4885        CH3    493    LEU    CD2   2100          0     15.035   ; qtot -1.94
  4886          C    493    LEU      C   2101       0.38     12.011   ; qtot -1.56
  4887          O    493    LEU      O   2101      -0.38    15.9994   ; qtot -1.94
  4888          N    494    ARG      N   2102      -0.28    14.0067   ; qtot -2.22
  4889          H    494    ARG      H   2102       0.28      1.008   ; qtot -1.94
  4890        CH1    494    ARG     CA   2103          0     13.019   ; qtot -1.94
  4891        CH2    494    ARG     CB   2103          0     14.027   ; qtot -1.94
  4892        CH2    494    ARG     CG   2103          0     14.027   ; qtot -1.94
  4893        CH2    494    ARG     CD   2104       0.09     14.027   ; qtot -1.85
  4894         NE    494    ARG     NE   2104      -0.11    14.0067   ; qtot -1.96
  4895          H    494    ARG     HE   2104       0.24      1.008   ; qtot -1.72
  4896          C    494    ARG     CZ   2104       0.34     12.011   ; qtot -1.38
  4897         NZ    494    ARG    NH1   2104      -0.26    14.0067   ; qtot -1.64
  4898          H    494    ARG   HH11   2104       0.24      1.008   ; qtot -1.4
  4899          H    494    ARG   HH12   2104       0.24      1.008   ; qtot -1.16
  4900         NZ    494    ARG    NH2   2104      -0.26    14.0067   ; qtot -1.42
  4901          H    494    ARG   HH21   2104       0.24      1.008   ; qtot -1.18
  4902          H    494    ARG   HH22   2104       0.24      1.008   ; qtot -0.94
  4903          C    494    ARG      C   2105       0.38     12.011   ; qtot -0.56
  4904          O    494    ARG      O   2105      -0.38    15.9994   ; qtot -0.94
  4905          N    495   LYSH      N   2106      -0.28    14.0067   ; qtot -1.22
  4906          H    495   LYSH      H   2106       0.28      1.008   ; qtot -0.94
  4907        CH1    495   LYSH     CA   2107          0     13.019   ; qtot -0.94
  4908        CH2    495   LYSH     CB   2107          0     14.027   ; qtot -0.94
  4909        CH2    495   LYSH     CG   2108          0     14.027   ; qtot -0.94
  4910        CH2    495   LYSH     CD   2108          0     14.027   ; qtot -0.94
  4911        CH2    495   LYSH     CE   2109      0.127     14.027   ; qtot -0.813
  4912         NL    495   LYSH     NZ   2109      0.129    14.0067   ; qtot -0.684
  4913          H    495   LYSH    HZ1   2109      0.248      1.008   ; qtot -0.436
  4914          H    495   LYSH    HZ2   2109      0.248      1.008   ; qtot -0.188
  4915          H    495   LYSH    HZ3   2109      0.248      1.008   ; qtot 0.06
  4916          C    495   LYSH      C   2110       0.27     12.011   ; qtot 0.33
  4917         OM    495   LYSH     O1   2110     -0.635    15.9994   ; qtot -0.305
  4918         OM    495   LYSH     O2   2110     -0.635    15.9994   ; qtot -0.94
  4919       MG2+    496     MG     MG   2111          2     24.305   ; qtot 1.06

there are so many non-integral charges here for  residues,
please help.
Thanks and regards 

--
Sonali Dhindwal

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