[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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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