[gmx-developers] Reading unprocessed topology files

Pedro Lacerda kanvuanza+gmx at zoho.com
Mon May 27 19:09:06 CEST 2013

---- On Mon, 27 May 2013 13:10:55 -0300 Mark Abraham<mark.j.abraham at gmail.com> wrote ---- 
On Mon, May 27, 2013 at 6:04 PM, Roland Schulz <roland at utk.edu> wrote:
 Do we have analysis tools which read topology from a top/itp file? I
 thought analysis tools always read it from the TPR.

IIRC genion touches the .top file, but I don't know if it parses much.

Yes. Seems that do_top() is intended for grompp and is the only way to read a top/itp file, other toolsparses just enough to do their jobs.

---- On Mon, 27 May 2013 13:04:53 -0300 Roland Schulz<roland at utk.edu> wrote ---- 
On Mon, May 27, 2013 at 9:56 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote: 
@Pedro: What is the reason you need to read a top file, and cannot 
generate a tpr first and then read it? 
Writing a .log file and read a .tpr was an artefact of the genion feature to place ions where the potentialsuggests (init_calcpot requires .tpr like). How this feature will be removed, genion could now read .top
files just like others preprocessing tools. However I'm happy to keep it reading preprocessed topologies.
If user supplies -table or -norandom, should genion die telling "foo option is depecrated"?


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