<!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;'><br><br><div id=""></div><br><div id="1"><br>---- On Mon, 27 May 2013 13:10:55 -0300 <b>Mark Abraham<mark.j.abraham@gmail.com></b> wrote ---- </div><blockquote style="border-left: 1px solid #0000FF; padding-left: 6px;"><div dir="ltr"><div>On Mon, May 27, 2013 at 6:04 PM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank" mailid="roland%40utk.edu" subj="">roland@utk.edu</a>></span> wrote:<br><div> <blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Do we have analysis tools which read topology from a top/itp file? I</div> thought analysis tools always read it from the TPR.<br></blockquote><div><br></div><div style="">IIRC genion touches the .top file, but I don't know if it parses much.</div></div></div></div></blockquote>Yes. Seems that do_top() is intended for grompp and is the only way to read a top/itp file, other tools<div>parses just enough to do their jobs.<br><div id=""></div><br><div id="1"><br>---- On Mon, 27 May 2013 13:04:53 -0300 <b>Roland Schulz<roland@utk.edu></b> wrote ---- </div><blockquote style="border-left-width: 1px; border-left-style: solid; border-left-color: rgb(0, 0, 255); padding-left: 6px;">On Mon, May 27, 2013 at 9:56 AM, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank" mailid="mark.j.abraham%40gmail.com" subj="">mark.j.abraham@gmail.com</a>> wrote: <br>@Pedro: What is the reason you need to read a top file, and cannot <br>generate a tpr first and then read it? <br></blockquote>Writing a .log file and read a .tpr was an artefact of the genion feature to place ions where the potential<div>suggests (init_calcpot requires .tpr like). How this feature will be removed, genion could now read .top</div><div>files just like others preprocessing tools. However I'm happy to keep it reading preprocessed topologies.</div><div>If user supplies -table or -norandom, should genion die telling "foo option is depecrated"?</div></div><div><br></div><div>Pedro</div></div></body></html>