[gmx-developers] Reading unprocessed topology files

Roland Schulz roland at utk.edu
Mon May 27 18:04:53 CEST 2013

On Mon, May 27, 2013 at 9:56 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> On Mon, May 27, 2013 at 3:40 AM, Pedro Lacerda <kanvuanza+gmx at zoho.com>

>> ## The question:
>> How can I read an topology file for populate my t_atoms (or gmx_mtop_t)
>> with eg. charges and masses? read_tpx() in tpxio.h can use only preprocessed
>> file formats like TPR. do_top() in topio.h seems a bit exagerated (in number
>> of function parameters) to just parse an TOP or ITP file and populate some
>> objects. If do_top() is the way to go, is grompp's new_status() approach
>> reasonable?
> The lack of modularity in this code is its most obvious quality. My usual
> recommendation for these kinds of questions is to pick a GROMACS tool that
> does something close to what you want, look at how it populates a data
> structure, do the same thing, and work out how to get the subset of data you
> really want. new_status() probably (over-)fills your needs.

Do we have analysis tools which read topology from a top/itp file? I
thought analysis tools always read it from the TPR.
@Pedro: What is the reason you need to read a top file, and cannot
generate a tpr first and then read it?


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