From: John Stone (
Date: Wed Oct 21 2020 - 13:44:04 CDT

The topotools tutorial here:

..suggests the common parameterization:
  topo somecommand someargument someotherargument [...] [-sel ] [-mol |top]

I think if you add -mol xxx, you should be in business.
I think that by default it operates on the top molecule.

  John Stone

On Fri, Oct 09, 2020 at 05:26:04PM +0100, fan li wrote:
> Dear VMD users
> I am using topo tools in vmd to generate input of lammps for bulk water. I
> have successfully get the correct angles and bonds information, but I
> found that the molecule ID is 1 for all molecules. Could anyone tell me
> how to set the molecule ID accordingly by topo tools?
> Thanks
> Fan

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