On Fri, May 17, 2013 at 4:28 PM, David Rosenman <[email protected]>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 <[email protected] > >wrote: > > > How does grompp -pp look? > > > > Mark > > > > > > On Fri, May 17, 2013 at 3:40 PM, davidjrosenman < > [email protected] > > >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 [email protected] > > > 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 [email protected]. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
