[gmx-users] how to set tolerance for bond formation distance?

Uwe Richter urichter at jerini.de
Thu Jun 23 09:06:26 CEST 2005


it's not quite clear what you mean. Gromacs doesn't  look at distances
to define bonds except for special bonds listed in the file specbond.dat.
Use chain id's in the pdb file. Otherwise chains will be connected no
matter what the distances are.


Kai Zhuang wrote:

>hi all,
>how do you adjust the distance between atoms at which gromacs consider
>a bond has been formed?
>i searched  the manual and can't seem to find the answer.
>specifically, i only want to do this for 4 residues, if that's possible
>more specifically, i want to prevent 2 bonds from forming.
>any ways i can do any of the above?
>thanks in advance =-)

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