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
