[gmx-users] graphene top file

[fatemeh ramezani]

Dear gmx-users
I built a graphene sheet (graphene.pdb ) by VMD. I convert it to gro file with editconf command. Then I made top file with g_x2top command. But in top file connection between atoms is not correct(highlighted lines below). How can I solve this problem?

Connection in pdb file for 12 atoms; 

CONECT    1    2
CONECT    2    1    3
CONECT    3    2    4
CONECT    4    3
CONECT    5    6
CONECT    6    5    7
CONECT    7    6    8
CONECT    8    7
CONECT    9   10
CONECT   10    9   11
CONECT   11   10   12


  Connection in top file for these atoms;
[ bonds ]
;  ai    aj      funct            c0            c1            c2            c3
    1     2        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
    1     6        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    1  1936      1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    2     3        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
    2    81       1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    3     4        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
    3    84       1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    4     7        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
    4    85       1  1.410000e-01  4.000000e+05  1.410000e-01  4.000000e+05 
    5     6        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
    5    10       1  1.410000e-01  4.000000e+05  1.410000e-01  4.000000e+05 
    5  1940      1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    6     7        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
    7     8        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    8    11        1  1.410000e-01  4.000000e+05  1.410000e-01  4.000000e+05 
    8    89        1  1.410000e-01  4.000000e+05  1.410000e-01  4.000000e+05 
    9    10        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
    9    14        1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    9  1944      1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
   10    11       1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
   11    12       1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 



Fatemeh Ramezani