<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, May 27, 2013 at 6:04 PM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">On Mon, May 27, 2013 at 9:56 AM, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a>> wrote:<br>
> On Mon, May 27, 2013 at 3:40 AM, Pedro Lacerda <<a href="mailto:kanvuanza%2Bgmx@zoho.com">kanvuanza+gmx@zoho.com</a>><br>
<br>
</div><div class="im">>> ## The question:<br>
>> How can I read an topology file for populate my t_atoms (or gmx_mtop_t)<br>
>> with eg. charges and masses? read_tpx() in tpxio.h can use only preprocessed<br>
>> file formats like TPR. do_top() in topio.h seems a bit exagerated (in number<br>
>> of function parameters) to just parse an TOP or ITP file and populate some<br>
>> objects. If do_top() is the way to go, is grompp's new_status() approach<br>
>> reasonable?<br>
><br>
><br>
</div><div class="im">> The lack of modularity in this code is its most obvious quality. My usual<br>
> recommendation for these kinds of questions is to pick a GROMACS tool that<br>
> does something close to what you want, look at how it populates a data<br>
> structure, do the same thing, and work out how to get the subset of data you<br>
> really want. new_status() probably (over-)fills your needs.<br>
<br>
</div>Do we have analysis tools which read topology from a top/itp file? I<br>
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 style><br></div><div style>Mark</div><div>
<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
@Pedro: What is the reason you need to read a top file, and cannot<br>
generate a tpr first and then read it?<br>
<br>
Roland<br>
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