[gmx-users] adding ions in Gromacs 4.6.5

[soumadwip ghosh]

Dear all,
              I am currently working on  double stranded DNA aggregation
and I require to add tetramethyl ammonium ions in my system. I know there
are certain files to be modified in the force field directory for this
purpose but I dont know which files. I am using Gromacs 4.6.5 and Charmm 27
forcefield. I created the following pdb file using Gauss view 5.0.8. I will
be highly obliged if someone tells me how and which files are to be
modified to run the simulations in presence of this ion,



TITLE       Required
REMARK   1 File created by GaussView 5.0.8
HETATM    1  N           0       3.666  -1.350  -1.577
  N
HETATM    2  C           0       4.157  -0.657  -2.777
  C
HETATM    3  H           0       5.227  -0.657  -2.777
  H
HETATM    4  H           0       3.800  -1.161  -3.651
  H
HETATM    5  H           0       3.800   0.352  -2.777
  H
HETATM    6  C           0       4.156  -0.657  -0.377
  C
HETATM    7  H           0       3.800   0.352  -0.377
  H
HETATM    8  H           0       3.800  -1.161   0.497
  H
HETATM    9  H           0       5.226  -0.657  -0.377
  H
HETATM   10  C           0       4.156  -2.736  -1.577
  C
HETATM   11  H           0       3.800  -3.240  -2.451
  H
HETATM   12  H           0       5.226  -2.736  -1.577
  H
HETATM   13  H           0       3.799  -3.240  -0.703
  H
HETATM   14  C           0       2.196  -1.350  -1.577
  C
HETATM   15  H           0       1.840  -0.341  -1.577
  H
HETATM   16  H           0       1.840  -1.854  -2.451
  H
HETATM   17  H           0       1.840  -1.854  -0.703
  H
END
CONECT    1    2    6   10   14
CONECT    2    1    3    4    5
CONECT    3    2
CONECT    4    2
CONECT    5    2
CONECT    6    1    7    8    9
CONECT    7    6
CONECT    8    6
CONECT    9    6
CONECT   10    1   11   12   13
CONECT   11   10
CONECT   12   10
CONECT   13   10
CONECT   14    1   15   16   17
CONECT   15   14
CONECT   16   14
CONECT   17   14

Thanks in advance
Soumadwip Ghosh
Senior research fellow,
Indian institute Of Technology, Bombay,
India