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

[Mark Abraham]

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
>