[gmx-users] .pdb to .gro => the atoms are not conneced with VMD

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 5 17:58:59 CEST 2008

Chih-Ying Lin wrote:
> Hi
> .pdb to .gro => the atoms are not conneced with VMD
>>From "Lu Tian"=>
> When .pdb convert to .gro,connecting information will lost,if the
> distance between two atoms in .gro is too long,they won't be
> connected.
> Can Gromacs recognize that they are connected from the .gro file?

When running a simulation, Gromacs recognizes bonds from the .top, which get 
passed to the .tpr when running grompp.

There is no connectivity information in the .gro by itself.


> Thank you
> Lin
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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