Hi Dulal,
So, my guess is you are trying to patch the installed plumed (not in root)
to AMBER 24. As I have suggested previously, you have to direct the missing
paths during configuration (PLUMED_LIBRARY, PLUMED_KERNEL_LIBRARY,
PLUMED_INCLUDES, PLUMED_WORKS). I don't think
"-DFORCE_EXTERNAL_LIBS=plumed" would do the thing you expect. Add those
paths to the run_make script and try again.
*Thanking you,*
*Yours sincerely,*
*Satyajit Khatua,*
*Post-doctoral fellow,*
*Department of Chemistry,*
*Georgia State University,*
*Atlanta, GA **30302.*
On Wed, Sep 18, 2024 at 1:13 AM Dulal Mondal <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> Dear Expert,
> I am trying to install amber24 patched with plumed in ubuntu 24.
> My run_cmake file is like below.
> cmake $AMBER_PREFIX/amber24_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
> -DCOMPILER=GNU \
> -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE -DBUILD_GUI=FALSE \
> -DDOWNLOAD_MINICONDA=TRUE -DFORCE_EXTERNAL_LIBS=plumed \
> 2>&1 | tee cmake.log
> The I do ./run_cmake
> The configuration is done. But I get the following error during
> configuration.
> CMake Error at AmberTools/src/sander/CMakeLists.txt:417 (add_library):
> Target "libsander" links to target "plumed::plumed" but the target was
> not
> found. Perhaps a find_package() call is missing for an IMPORTED target,
> or
> an ALIAS target is missing?
>
>
> CMake Error at AmberTools/src/sander/CMakeLists.txt:434 (add_library):
> Target "libsanderles" links to target "plumed::plumed" but the target was
> not found. Perhaps a find_package() call is missing for an IMPORTED
> target, or an ALIAS target is missing?
>
>
> CMake Error at AmberTools/src/sander/CMakeLists.txt:417 (add_library):
> Target "libsander" links to target "plumed::plumed" but the target was
> not
> found. Perhaps a find_package() call is missing for an IMPORTED target,
> or
> an ALIAS target is missing?
>
>
> CMake Error at AmberTools/src/sander/CMakeLists.txt:434 (add_library):
> Target "libsanderles" links to target "plumed::plumed" but the target was
> not found. Perhaps a find_package() call is missing for an IMPORTED
> target, or an ALIAS target is missing?
>
>
> CMake Error at AmberTools/src/sander/CMakeLists.txt:366 (add_executable):
> Target "sander" links to target "plumed::plumed" but the target was not
> found. Perhaps a find_package() call is missing for an IMPORTED target,
> or
> an ALIAS target is missing?
>
>
> CMake Error at AmberTools/src/sander/CMakeLists.txt:386 (add_executable):
> Target "sander.LES" links to target "plumed::plumed" but the target was
> not
> found. Perhaps a find_package() call is missing for an IMPORTED target,
> or
> an ALIAS target is missing?
>
>
> CMake Error at AmberTools/src/cpptraj/src/CMakeLists.txt:130
> (add_executable):
> Target "cpptraj" links to target "plumed::plumed" but the target was not
> found. Perhaps a find_package() call is missing for an IMPORTED target,
> or
> an ALIAS target is missing?
>
>
> CMake Error at src/pmemd/src/CMakeLists.txt:218 (add_executable):
> Target "pmemd.decomp" links to target "plumed::plumed" but the target was
> not found. Perhaps a find_package() call is missing for an IMPORTED
> target, or an ALIAS target is missing?
>
>
> CMake Error at src/pmemd/src/CMakeLists.txt:192 (add_executable):
> Target "pmemd" links to target "plumed::plumed" but the target was not
> found. Perhaps a find_package() call is missing for an IMPORTED target,
> or
> an ALIAS target is missing?
> I also uploaded the cmake.log file.
>
>
>
> On Mon, Sep 16, 2024 at 9:40 PM Dulal Mondal <
> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>
>> Thank you for the clarification.
>>
>> On Mon, 16 Sept 2024, 9:06 pm SATYAJIT KHATUA, <
>> satyajitkhatua09.gmail.com> wrote:
>>
>>> Hi Dulal,
>>>
>>> Install it as a root if you have sudo privilege. Otherwise, you have to
>>> direct the plumed libraries and kernel paths that were asked during
>>> configuration (with -D option).
>>>
>>> *Best,*
>>> *Satyajit Khatua*
>>>
>>>
>>> On Mon, Sep 16, 2024 at 10:07 AM Dulal Mondal via AMBER <
>>> amber.ambermd.org> wrote:
>>>
>>>> Dear Experts,
>>>> How I patched plumed with amber24.
>>>>
>>>> In general plumed shows in disabled category.
>>>> ---disabled: ------------------------------------------------
>>>> -- c9x-complex - used as a support library on systems that do not have
>>>> C99
>>>> complex.h support
>>>> -- protobuf - protocol buffers library, used for communication with
>>>> external software in QM/MM
>>>> -- lio - used by Sander to run certain QM routines on the GPU
>>>> -- apbs - used by Sander as an alternate Poisson-Boltzmann equation
>>>> solver
>>>> -- pupil - used by Sander as an alternate user interface
>>>> -- plumed - used as an alternate MD backend for Sander
>>>> --
>>>> *With regards,*
>>>> *Dulal Mondal,*
>>>> *Research Scholar,*
>>>> *Department of Chemistry,*
>>>> *IIT Kharagpur, Kharagpur 721302.*
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 18 2024 - 00:30:02 PDT
