Segmentation Fault (core dumped) error.

[Sanket Ghawali]

Hello,

I follow the procedures of installation g_mmpbsa from source code. (website:http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html)
I have installed gromacs 5.1.1 and then I installed g_mmpbsa without APBS (to use with external APBS).

g_mmpbsa, VERSION 5.1.2

Commands use for installation

tar -zxvf g_mmpbsa.tar.gz
cd bin
sudo cp g_mmpbsa /usr/local/bin/.
sudo cp energy2bfac /usr/local/bin/.

cd RashmiKumari-g_mmpbsa-160f685
mkdir build
cd build

export CMAKE_PREFIX_PATH=/usr/local/gromacs

cmake -DEXT_APBS=on \

-DCMAKE_INSTALL_PREFIX=/root/Downloads/RashmiKumari-g_mmpbsa-160f685 \

-DFFTW_LIB=/root/Downloads/gromacs-5.1.1/build/src/contrib/fftw/fftwBuild-prefix/lib \
..

When I execute MM and apolar calculations, there is no problem.

But when I execute polar calculations, I get Segmentation Fault (core
dumped) error.

I tried the tutorial files, and getting the same error in polar
calculations.

Error:
Command line:
g_mmpbsa -f ../data/1EBZ.xtc -s ../data/1EBZ.tpr -n ../data/1EBZ.ndx -i mmpbsa.mdp -nomme -pbsa -decomp


:-) g_mmpbsa (-:

Authors: Rashmi Kumari and Andrew Lynn
Contribution: Rajendra Kumar

Copyright (C) 2013 - 2016 Rashmi Kumari and Andrew Lynn

g_mmpbsa is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

g_mmpbsa is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with g_mmpbsa. If not, see <http://www.gnu.org/licenses/>.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

:-) g_mmpbsa (-:
Reading file ../data/1EBZ.tpr, VERSION 4.5.5-dev-20110921-e25c350 (single precision)
Reading file ../data/1EBZ.tpr, VERSION 4.5.5-dev-20110921-e25c350 (single precision)



Enter the group number for Protein or first Protein or first group:
Group 0 ( System) has 3218 elements
Group 1 ( Protein) has 3129 elements
Group 2 ( Protein-H) has 1516 elements
Group 3 ( C-alpha) has 198 elements
Group 4 ( Backbone) has 594 elements
Group 5 ( MainChain) has 794 elements
Group 6 ( MainChain+Cb) has 966 elements
Group 7 ( MainChain+H) has 984 elements
Group 8 ( SideChain) has 2145 elements
Group 9 ( SideChain-H) has 722 elements
Group 10 ( Prot-Masses) has 3129 elements
Group 11 ( non-Protein) has 89 elements
Group 12 ( Other) has 89 elements
Group 13 ( BEC) has 89 elements
Select a group: 1
Selected 1: 'Protein'



Enter the group number of Ligand or second Protein or second group:
Group 0 ( System) has 3218 elements
Group 1 ( Protein) has 3129 elements
Group 2 ( Protein-H) has 1516 elements
Group 3 ( C-alpha) has 198 elements
Group 4 ( Backbone) has 594 elements
Group 5 ( MainChain) has 794 elements
Group 6 ( MainChain+Cb) has 966 elements
Group 7 ( MainChain+H) has 984 elements
Group 8 ( SideChain) has 2145 elements
Group 9 ( SideChain-H) has 722 elements
Group 10 ( Prot-Masses) has 3129 elements
Group 11 ( non-Protein) has 89 elements
Group 12 ( Other) has 89 elements
Group 13 ( BEC) has 89 elements
Select a group: 13
Selected 13: 'BEC'
Reading frame 0 time 0.000 Segmentation fault (core dumped)

Please Help

Thanks & Regards
Sanket

[Nikhil M]

HI,

What is your OS?

try to install from precompiled executable program with includes APBS functionality 

[Sanket Ghawali]

 HI,
Thank you Nikhil M for the reply

I am working on CentOS 7

[Samuel Silva da Rocha Pita]

Dear g_mmpbsa user, good afternoon.

 I'd tried to run g_mmpbsa precompiled on versions 5.0.x and 5.1.x, both 64-bit and both gave me the same error:

This executable compiled on Apr 19 2016 at 23:49:12
Parsing input file pVZLaSsA.in...
 Since I'm running locally on an Oracle Linux 8.8, 64-bit, 16-core, and the error remains the same despite I'm using the test/data files (i.e., EBZ files and polar_orig/mmpbsa.mdp), I wonder how I can solve this issue and run g_mmpbbsa in my system (3374 prot+lig atoms)?

 Regards.