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

[David van der Spoel]

darrellk at 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se