Re: [gmx-users] Message-ID:

[Justin Lemkul]

On 9/20/18 5:01 PM, BIJENDRA KHADKA wrote:

  Dear Justin,
Thank you for your suggestion. I tried to process the ligand(NAD) with
pdb2gmx, however, received the following error despite correct atom name in
PDB file (file attached) relative to NAD information in merged.itp.
In case of CHARMM-GUI, it provides a NAD.rtf and .prm as output, while
Gromacs required an .itp as input. (How to convert .rtf file to .itp file).


You can't; a CHARMM .rtf is the equivalent of a GROMACS .rtp, not .itp. 
Besides, CHARMM-GUI provides you with all the files you need to run in 
GROMACS. Don't try to re-execute pdb2gmx. Just use the files it gives you.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] Message-ID:

[BIJENDRA KHADKA]

 Dear Justin,
Thank you for your suggestion. I tried to process the ligand(NAD) with
pdb2gmx, however, received the following error despite correct atom name in
PDB file (file attached) relative to NAD information in merged.itp.
In case of CHARMM-GUI, it provides a NAD.rtf and .prm as output, while
Gromacs required an .itp as input. (How to convert .rtf file to .itp file).

Command: /gmx pdb2gmx -f NAD.pdb -i NAD.itp

Fatal error:
Atom HN in residue NAD 1 was not found in rtp entry NAD with 70 atoms
while sorting atoms.

KInd Regards,


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[gmx-users] Message-ID:

[Kim Jessica Novacek]

Hey Mark,
I tried to set the CMAKE_LIBRARY_PATH to an actual file, because it cannot be 
found by cmake if I left it out, but it is there.
Greetings Kim
 
> > Ursprüngliche Nachricht:
> > Von: Kim Jessica Novacek 
> > An: gromacs.org_gmx-users@maillist.sys.kth.se
> > Kopie: 
> > Datum: Mon Oct 12 15:31:58 CEST 2015
> > 
> > Although I did let out the Xeon Phi Command there is still the same make 
> > error.
> > Greetings 
> > Kim
> > 
> > 
> > /usr/bin/ld: cannot find -lcudart
> > /usr/bin/ld: cannot find -lmpi
> > collect2: error: ld returned 1 exit status
> > make[2]: *** [bin/gmx_mpi] Fehler 1
> > make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2
> > make[1]: *** Auf noch nicht beendete Prozesse wird gewartet …
> > /usr/bin/ld: cannot find -lcudart
> > /usr/bin/ld: cannot find -lmpi
> > collect2: error: ld returned 1 exit status
> > make[2]: *** [bin/template] Fehler 1
> > make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2
> > make: *** [all] Fehler 2
> > 
> > 
> > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc 
> > -DGMX_MPI=ON
> > -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit 
> > -DCMAKE_INSTALL_PREFIX=/usr
> /l
> > ocal/GROMACS -DGMX_FFT_LIBRARY=fftw3 
> > -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a
> -DCMAKE_BUILD_T
> > YPE=DEBUG -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON 
> > -DCMAKE_C_FLAGS="-sta
> ti
> > c" -DCMAKE_CXX_FLAGS="-static" -DCMAKE_SKIP_RPATH=YES 
> > -DCMAKE_PREFIX_PATH=/usr/lib/cuda
> > -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so 
> > -DCMAKE_PREFIX_PATH=/usr/include/
> li
> > bxml2/libxml
>
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[gmx-users] Message-ID:

[Kim Jessica Novacek]

Although I did let out the Xeon Phi Command there is still the same make error.
Greetings 
Kim


/usr/bin/ld: cannot find -lcudart
/usr/bin/ld: cannot find -lmpi
collect2: error: ld returned 1 exit status
make[2]: *** [bin/gmx_mpi] Fehler 1
make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2
make[1]: *** Auf noch nicht beendete Prozesse wird gewartet …
/usr/bin/ld: cannot find -lcudart
/usr/bin/ld: cannot find -lmpi
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Fehler 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2
make: *** [all] Fehler 2


cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc 
-DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit 
-DCMAKE_INSTALL_PREFIX=/usr/local/GROMACS -DGMX_FFT_LIBRARY=fftw3 
-DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a -DCMAKE_BUILD_TYPE=DEBUG 
-DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON 
-DCMAKE_C_FLAGS="-static" -DCMAKE_CXX_FLAGS="-static" -DCMAKE_SKIP_RPATH=YES 
-DCMAKE_PREFIX_PATH=/usr/lib/cuda 
-DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so 
-DCMAKE_PREFIX_PATH=/usr/include/libxml2/libxml
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Re: [gmx-users] Message-ID:

[Mark Abraham]

Hi,

On Mon, Oct 12, 2015 at 3:31 PM Kim Jessica Novacek <
kim.j.nova...@campus.lmu.de> wrote:

> Although I did let out the Xeon Phi Command there is still the same make
> error.
> Greetings
> Kim
>
>
> /usr/bin/ld: cannot find -lcudart
> /usr/bin/ld: cannot find -lmpi
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/gmx_mpi] Fehler 1
> make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2
> make[1]: *** Auf noch nicht beendete Prozesse wird gewartet …
> /usr/bin/ld: cannot find -lcudart
> /usr/bin/ld: cannot find -lmpi
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Fehler 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2
> make: *** [all] Fehler 2
>
>
> cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc
> -DGMX_MPI=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit
> -DCMAKE_INSTALL_PREFIX=/usr/local/GROMACS -DGMX_FFT_LIBRARY=fftw3
> -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a -DCMAKE_BUILD_TYPE=DEBUG
> -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON
> -DCMAKE_C_FLAGS="-static" -DCMAKE_CXX_FLAGS="-static"
> -DCMAKE_SKIP_RPATH=YES -DCMAKE_PREFIX_PATH=/usr/lib/cuda
> -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so
> -DCMAKE_PREFIX_PATH=/usr/include/libxml2/libxml
>

Setting CMAKE_LIBRARY_PATH to an actual file, which is then the one that
can't be found seems like a bad thing to do. That path is a standard system
path, so if you want to find that library, you can probably leave it alone.
But you will get this library via the CUDA toolkit you already asked for,
if the toolkit is installed correctly and you're using it the way the
sysadmins intended you to use it.

Your system should have an MPI wrapper compiler - find out what it is and
use it. Maybe there's even a documented way to compile for MPI+CUDA :-)

Mark


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