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

[David Rosenman]

This is a good idea, but it doesn't work. It produces a more detailed .top
file with force field parameters, but still, only the connectivities of the
protein are provided. top2psf has no idea what to do with this file, by the
way.

Would it help for me to provide the pre-processed and post-processed top
files?

Cheers,
David


On Fri, May 17, 2013 at 10:17 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> How does grompp -pp look?
>
> Mark
>
>
> 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
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
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