darre...@ece.ubc.ca wrote:
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?
You can turn off parameter printing with a flag. They are double to
specify that A & B are the same, otherwise it may be interpreted as FEP
input.
You have to manually fix atomtypes and charges anyway.
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
************************************************************************
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