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

[David Rosenman]

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.

Cheers,
David



On Sat, May 18, 2013 at 3:07 PM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:

>
> Or just do it by hand and replace the lines in the .top with each protein
> chains .itp file.
>
> Stephan
>  *Gesendet:* Freitag, 17. Mai 2013 um 16:17 Uhr
> *Von:* "Mark Abraham" <mark.j.abraham at gmail.com>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* Re: [gmx-users] Expanding a .top file to have all connection
> information
> 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
>