<div dir="ltr">On Fri, Aug 14, 2015 at 1:24 AM Ondrej Marsalek <<a href="mailto:ondrej.marsalek@gmail.com">ondrej.marsalek@gmail.com</a>> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">However, I lost the ability to get the documentation using the -h<br>
option. Other common arguments, like -b and -e, work fine (I give<br>
PCA_CAN_TIME to parse_common_args). Is there some obvious change in<br>
version 5 that I am missing that is causing this, or do I need to dig<br>
deeper?</blockquote><div> </div><div>You need to use gmx_run_cmain() as a wrapper around your old main() function. And you need to respect the return value of parse_common_args() if you didn't yet do that change.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Another problem is that where I was previously (with 4.6) able<br>
to provide a .tpr and only optionally an .ndx, if I now only give a<br>
.tpr, the program fails with:<br>
<br>
-------------------------------------------------------<br>
Program GROMACS, VERSION 5.0.2<br>
Source code file:<br>
/home/marsalek/build/gromacs-5.0.2/src/gromacs/fileio/futil.cpp, line:<br>
790<br>
<br>
Fatal error:<br>
Library file residuetypes.dat not found in current dir nor in default<br>
directories.<br>
(You can set the directories to search with the GMXLIB path variable)<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" rel="noreferrer" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
when get_index is called. If I copy residuetypes.dat to the working<br>
directory, the tool runs fine. Other GROMACS tools also work as<br>
expected.<br></blockquote><div><br></div><div>When you start using gmx_run_cmain(), the tool will by default also print out the library directory from where it looks for residuetypes.dat. That may help diagnosing the issue, but not knowing your directory structure or the way you compiled/installed Gromacs or your tool, I can't immediately suggest any possible reason.</div><div><br></div><div>Best regards,</div><div>Teemu</div></div></div>