[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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