[gmx-developers] Compiling analysis tool with GROMACS 5

Ondrej Marsalek ondrej.marsalek at gmail.com
Fri Aug 14 00:23:55 CEST 2015

Dear GROMACS developers,

I have a custom analysis tool that worked with 4.6 and I am trying to
make it work with GROMACS 5. I had to tweak a couple of function calls
with changed signatures but with that, the analysis itself works.
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? 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:

Fatal error:
Library file residuetypes.dat not found in current dir nor in default
(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

The analysis code is "old style" for now. I plan to convert it to the
new analysis framework eventually, but for now would like to get it
working properly as is.

Thank you for any suggestions,

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