[gmx-developers] Reading unprocessed topology files

Pedro Lacerda kanvuanza+gmx at zoho.com
Mon May 27 03:40:39 CEST 2013

Hello all,

I met gromacs and molecular dynamics an year ago for my undergrad project. I know next to nothing about biochemistry or physics but I'm able to program in Python and trying to learn C/C++ with gromacs. Because I'm from Bahia-Brazil my native language is portuguese, and I did really bad on english courses, sometimes I can misunderstand you or explain myself in a confusing manner.

Recently I fixed two bugs in genion (really wasn't me but the reviewers :) Fix -neutral option in genion and Fix genion -nq and -pq when using -neutral, saw bug #615, and felt me adventurous.

## 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?

Sorry if someone already asked this, I didn't found in the archives.

Pedro Lacerda
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