[gmx-users] Segmentation Fault (core dumped) in g_mmpbsa polar energy calculation
Pavithra
meetpavithramsc at gmail.com
Wed Jun 1 10:16:19 CEST 2016
Dear users,
I have installed g_mmpbsa package for MMPBSA calculation in gromacs.
When I execute MM 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.
The exact output is below.
[pavithra at biopo3 1EBZ]$ g_mmpbsa -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i
../polar.mdp -nomme -pbsa -decomp
:-) g_mmpbsa (-:
Authors: Rashmi Kumari and Andrew Lynn
Contribution: Rajendra Kumar
Copyright (C) 2013 - 2015 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 (-:
Option Filename Type Description
------------------------------------------------------------
-f 1EBZ.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-s 1EBZ.tpr Input Run input file: tpr tpb tpa
-i ../polar.mdp Input, Opt! grompp input file with MD parameters
-n 1EBZ.ndx Input, Opt! Index file
-mm energy_MM.xvg Output, Opt. xvgr/xmgr file
-pol polar.xvg Output, Opt. xvgr/xmgr file
-apol apolar.xvg Output, Opt. xvgr/xmgr file
-mmcon contrib_MM.dat Output, Opt. Generic data file
-pcon contrib_pol.dat Output, Opt. Generic data file
-apcon contrib_apol.dat Output, Opt. Generic data file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]silent bool no Display messages, output and errors from
external
APBS program. Only works with external APBS
program
-rad enum bondi van der Waal radius type: bondi, mbondi, mbondi2
or force-field
-rvdw real 0.1 Default van der Waal radius (in nm) if radius
not
found for any atom-types
-[no]mme bool no To calculate vacuum molecular mechanics energy
-pdie real 1 Dielectric constant of solute. Should be same as
of polar solvation
-[no]incl_14 bool no Include 1-4 atom-pairs, exclude 1-2 and 1-3 atom
pairs during MM calculation. Should be "yes"
when
groups are bonded with each other.
-[no]focus bool no To enable focusing on the specfic region of
molecule, group of atoms must be provided in
index file
-[no]pbsa bool yes To calculate polar and/or non-polar solvation
energy
-ndots int 24 Number of dots per sphere in the calculation of
SASA, more dots means more accuracy
-[no]diff bool yes Calculate the energy difference between two
group
otherwise only calculates for one group
-[no]decomp bool yes Decomposition of energy for each residue
Reading file 1EBZ.tpr, VERSION 4.5.5-dev-20110921-e25c350 (single precision)
Reading file 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
Back Off! I just backed up polar.xvg to ./#polar.xvg.1#
Back Off! I just backed up contrib_pol.dat to ./#contrib_pol.dat.1#
Segmentation fault (core dumped)
I searched for the solution and found it could be memory allocation
problem. How to be sure if its memory problem (I'm running this in centos
desktop).
Mine is 5ns simulation (xtc file)
please help.
regards,
Pavithra.
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