[gmx-users] Topology file

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 2 21:46:34 CET 2015

Hi Michelle,

You should only change the moleculetype definition. Delete the
pairs/bonds/angles/dihedrals sections there, so you're only left with the
atom listing and the position restraints.


On Jan 2, 2015 9:32 PM, "Aranha, Michelle" <maranha at vols.utk.edu> wrote:

> Hi,
> I wanted to create a topology file without the bonds, angles and dihedrals
> for a CNT fixed in space using position restraints. I use the g_x2top
> program for building the topology. My understanding was that if I comment
> out the #include ffbonded.itp in the forcefield.itp file. I should have a
> topology file without bonds, angles and dihedrals. However, the topology
> file I get has all bonds, angles and dihedrals. I also tried deleting the
> ffbonded.itp file from the directory but got the same result. I am not sure
> how the program works. I understand that I can edit out the bonds, angles
> and dihedrals lines in topology file, but I would just like to know how
> does the program generate the topology file even when I don't specify the
> bonded parameters.
> Best regards,
> Michelle
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