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
