[gmx-developers] Compiling analysis tool with GROMACS 5

Teemu Murtola teemu.murtola at gmail.com
Fri Aug 14 05:09:15 CEST 2015

On Fri, Aug 14, 2015 at 1:24 AM Ondrej Marsalek <ondrej.marsalek at gmail.com>

> However, I lost the ability to get the documentation using the -h
> option. Other common arguments, like -b and -e, work fine (I give
> PCA_CAN_TIME to parse_common_args). Is there some obvious change in
> version 5 that I am missing that is causing this, or do I need to dig
> deeper?

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.

Another problem is that where I was previously (with 4.6) able
> to provide a .tpr and only optionally an .ndx, if I now only give a
> .tpr, the program fails with:
> -------------------------------------------------------
> Program GROMACS, VERSION 5.0.2
> Source code file:
> /home/marsalek/build/gromacs-5.0.2/src/gromacs/fileio/futil.cpp, line:
> 790
> Fatal error:
> Library file residuetypes.dat not found in current dir nor in default
> directories.
> (You can set the directories to search with the GMXLIB path variable)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> when get_index is called. If I copy residuetypes.dat to the working
> directory, the tool runs fine. Other GROMACS tools also work as
> expected.

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.

Best regards,
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