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

Mark Abraham mark.j.abraham at gmail.com
Fri May 17 16:17:10 CEST 2013

How does grompp -pp look?


On Fri, May 17, 2013 at 3:40 PM, davidjrosenman <davidjrosenman at gmail.com>wrote:

> Hello everyone,
> This may be a bit out of the purview of this list, but it can't hurt to
> ask.
> Let me start from the beginning: I'm trying to take a structure/topology
> that I generated with GROMACS tools and convert it to run with NAMD. The
> problem is that this is a huge simulation box with many different atom
> types
> (homodimeric protein, water, lipids, ions), and I am having a lot of
> trouble
> generating a .psf file from the information I have.
> The current strategy I'm pursuing to accomplish this task is to use the
> top2psf script:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/
> The issue is that this script will only read what is explicitly written in
> the top file. All of the include records will be ignored, as will multiple
> molecules. So, the output is a psf suitable ONLY for the first chain of my
> dimer. I want a psf that will include all components of my structure,
> including the lipids, waters, etc.
> So, I ask, is there a way to expand a topology to explicitly get all of the
> connectivities in a structure? I figure this information must be contained
> in the .tpr file, but that's neither human readable nor compatible with
> top2psf.
> If you have any advice for that, or for the larger problem at hand, I would
> appreciate it. Thank you very much!
> Cheers,
> David Rosenman
> Grad Student, Rensselaer Polytechnic Institute
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Expanding-a-top-file-to-have-all-connection-information-tp5008345.html
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