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

davidjrosenman davidjrosenman at gmail.com
Fri May 17 15:40:38 CEST 2013

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: 

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

If you have any advice for that, or for the larger problem at hand, I would
appreciate it. Thank you very much! 

David Rosenman 
Grad Student, Rensselaer Polytechnic Institute

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