<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><html><head><meta content="text/html;charset=UTF-8" http-equiv="Content-Type"></head><body ><div style='font-size:10pt;font-family:Verdana,Arial,Helvetica,sans-serif;'>Hello all,<div><br></div><div>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.</div><div><br></div><div>Recently I fixed two bugs in genion (really wasn't me but the reviewers :) <a href="https://gerrit.gromacs.org/#q,I08b019b05cf3d8511757c4665c24dcaa37968ceb,n,z" target="_blank">Fix -neutral option in genion</a> and <a href="https://gerrit.gromacs.org/#q,If2a82ace079555d8a684ea876daa947677d5e442,n,z" target="_blank">Fix genion -nq and -pq when using -neutral</a>, saw <a href="http://redmine.gromacs.org/issues/615" target="_blank">bug #615</a>, and felt me adventurous.</div><div><br></div><div>## The question:</div><div>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?</div><div><br></div><div>Sorry if someone already asked this, I didn't found in the archives.</div><div><br></div><div>--</div><div>abraços,</div><div>Pedro Lacerda</div> </div></body></html>