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

[Mark Abraham]

On Fri, May 17, 2013 at 4:28 PM, David Rosenman <davidjrosenman at gmail.com>wrote:

> 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.


What "connectivities" are missing?


> 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?
>

Sure, but attachments will generally be rejected. Use a file sharing
service.

Mark


>
> 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.
> > > --
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>