Topology viewer

User discussions
1

GROMACS version: 2021.3
GROMACS modification: No

I am building a complex topology by hand, assembling fragments from several different reported topologies. In doing so, I would like to do two things:

  1. Find relevant fragments in the reported topology files
  2. Check for correctness of bonds in the assembled topology file

Doing all this work on paper (drawing structure, finding bonds and atom name assignments) is extremely cumbersome. The same difficulties apply to the assembled topology as well.

I was wondering if there is a tool available which can load itp/top files and display the structure. Or, can the itp/top be converted to a gro/pdb file so I can view it in VMD? There is no gro/pdb available for the reported topologies.

Thanks,
Raman

2

For complex topology operations, such as adding or removing bonds, I can recommend gromologist - it doesn’t display the molecule but has a set of basic routines for topology manipulation, adding parameters/labels etc. I wrote it exactly out of frustration of having to draw/reassign atoms on paper even with moderately simple modifications ;)

If you need some specific routines that are not available, I can also add them to the code.