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

[Mark Abraham]

Hi,

On Fri, Jul 3, 2015 at 12:48 PM Hassan Aaryapour <hassan.gromacs at gmail.com>
wrote:

> 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.


Don't do that. We've made hundreds of changes all over the place since
then. The error you saw is just the first iceberg (and not just its tip!)
;-)

You can
a) get a complete copy of working code from that link
b) do a git checkout the GROMACS master branch since that code is now merged
c) wait for the release candidate of 5.1 (any day now)

Mark

for installing I obtained below error in
> "make" step.
>
>  $ cmake .. -DGMX_BUILD_OWN_FFTW=ON
>
> $ make -j 8
>
> ....
>
> [ 5%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.c.o
>
>
> /home/qmmm/Documents/Softs/gromacs-5.0.5/src/gromacs/gmxpreprocess/topio.c:37:20:
> 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
>
> Hassan
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