[gmx-users] Install gromacs with intermolecular bonded interaction support

Hassan Aaryapour hassan.gromacs at gmail.com
Fri Jul 3 12:47:50 CEST 2015

Dear Gromacs-Users,

I want to do a gromacs installation with intermolecular bonded interaction
support to apply a weak repulsive potential between ligands to avoid
aggregation. All of the patches in this URL (
https://gerrit.gromacs.org/#/c/2566/) were added or replaced with original
files in source of gromacs-5.0.5. for installing I obtained below error in
"make" step.


$ make -j 8


[ 5%] Building C object

fatal error: gmxpre.h: No such file or directory

#include "gmxpre.h"


compilation terminated.

src/gromacs/CMakeFiles/libgromacs.dir/build.make:537: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.c.o' failed

make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.c.o] Error 1

make[2]: *** Waiting for unfinished jobs....

CMakeFiles/Makefile2:1653: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed

make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2

Makefile:146: recipe for target 'all' failed

make: *** [all] Error 2

 I would greatly appreciate if someone could help me to resolve this error.

Best Wishes


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