[gmx-users] Expanding a .top file to have all connection information
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:
> The grompp -pp processed top is:
> 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
>>> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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