[gmx-users] x2top: duplicate bond, angle, & dihedral parameters; missing VdW parameters

[darrellk at ece.ubc.ca]

Dear All,
I ran the x2top command and successfully generated a topology. However,
the topology file has duplicate bond, angle, and dihedral parameters and
missing Van der Waals parameters. I am including sections of my topology
file for your perusal. Please let me know why this is occurring and how
to solve this problem?

Much thanks.

Darrell

************************************************************************
Command issued (Note: I selected the oplsaa option):
x2top -ff select -f graphene_nm.gro -o graphene_nm.top
************************************************************************
Selected segments from graphene_nm.top file:
[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1    11     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2        
   c3
    2     1     3     1  1.200000e+02  4.000000e+02  1.200000e+02 
4.000000e+02

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2  
         c3            c4            c5
    3     1     2     5     3  3.600000e+02  5.000000e+00  3.000000e+00 
3.600000e+02  5.000000e+00  3.000000e+00
************************************************************************
Selected segments from graphene_nm.top file(for reference):
MD of Graphene, t=0.0
     270
    2Grph C        1   0.000   0.000   0.000  0.0000  0.0000  0.0000
    2Grph C        2   0.071  -0.123   0.000  0.0000  0.0000  0.0000
    2Grph C        3   0.071   0.123   0.000  0.0000  0.0000  0.0000
************************************************************************