[gmx-users] Expanding a .top file to have all connection information

Justin Lemkul jalemkul at vt.edu
Mon May 20 04:49:58 CEST 2013

On 5/19/13 10:36 PM, David Rosenman wrote:
> Hello again,
> Sorry for the delay in my response.
> The original top file is:
> http://wikisend.com/download/951610/APPTM_WT.top
> The grompp -pp processed top is:
> http://wikisend.com/download/851584/APPTM_WT_processed.top
> The connectivities that are not explicitly mentioned in either of these
> files are the connections between the second molecule of the homodimer,
> between all DPC detergent molecules, and between all water molecules.
> GROMACS already knows what the connectivities of these are because it can
> interpret both included itp files and multiple molecules. But, top2psf
> doesn't.
>>> Or just do it by hand and replace the lines in the .top with each
> protein chains .itp file.
> This won't work because the generalized atom indices in the itp files don't
> match the actual atom indices in the structure for each molecule I need
> included.  And there are many molecules to deal with here. . .ie, 100000
> water molecules! I suppose one could write a script to make the
> translation, but it sounds like it may be a challenging task.

If all of your molecules are described by .rtp entries, you can re-run pdb2gmx 
on the completed system, applying some suitable option to -chainsep to create 
new [moleculetypes] for every molecule present.  The topology will be very 
redundant, but it may give you what you want.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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