Calculations do not finish
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Flavio Seixas
Nov 8, 2014, 11:01:16 AM11/8/14
to g_mm...@googlegroups.com
Hi,
I install g_mmpbsa from source in a CentosOS 6.5 64bits and also in a Fedora 20 64bits. Both systems have Gromacs 4.5
The tutorial works very fine and was fully completed.
But, when I was trying to use in my sistem (lysozyme inhibitor system in a cubic box with NaCl 0.15M neutral charges), the calculations not finishes. The program does not finishes properly. The last lines at shell are:
----------------------------------------
CALCULATION #4 (mol2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (1.81 A) for exclusion function
Debye length: 0.889267 A
Current memory usage: 297.746 MB total, 331.000 MB high water
Grid dimensions: 97 x 97 x 129
Grid spacings: 0.497 x 0.505 x 0.457
Grid lengths: 47.710 x 48.480 x 58.440
Grid center: (38.385, 39.670, 38.320)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
0.950 A-radius, 1.000 e-charge, 0.150 M concentration
1.810 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Solving PDE (see io.mc* for details)...
Calculating energy (see io.mc* for details)...
Total electrostatic energy = 6.901516896524E+04 kJ/mol
Fixed charge energy = 69015.2 kJ/mol
Mobile charge energy = 233.268 kJ/mol
Dielectric energy = 49294 kJ/mol
Per-atom energies:
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (mol1) - 2 (mol2) end
Local net energy (PE 0) = -6.601057266615E+03 kJ/mol
Global net ELEC energy = -6.601057266615E+03 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 331.000 MB high water
Thanks for using APBS!
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 1.3
Nathan A. Baker (nathan...@pnl.gov)
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of Washington University in St. Louis nor the names of its
contributors may be used to endorse or promote products derived from this
software without specific prior written permission.
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.
----------------------------------------------------------------------
APBS uses FETK (the Finite Element ToolKit) to solve the
Poisson-Boltzmann equation numerically. FETK is a portable collection
of finite element modeling class libraries developed by the Michael Holst
research group and written in an object-oriented form of C. FEtk is
designed to solve general coupled systems of nonlinear partial differential
equations using adaptive finite element methods, inexact Newton methods,
and algebraic multilevel methods. More information about FEtk may be found
at <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2014 at 14:56:24
Parsing input file pw8DCiRA.in...
NOsh: Deprecated use of ION keyword! Use key-value pairs
NOsh: Deprecated use of ION keyword! Use key-value pairs
I understand "NOsh: Deprecated use of ION keyword! Use key-value pairs" is just a warning, but the program are at this stage more than 24 hours in a quad-core machine.
At the biegining of calculations all processors was used, but in this last stage, only one processor are running for more than 24 hours.
The tutorial was finished in less than 10 minuts.
The output files apolar.xvg and polar.xvg contains only part of the 51 frames (0.1 ns):
APOLAR.XVG
# This file was created Sat Nov 8 09:43:38 2014
# by the following command:
# g_mmpbsa -f DINAMICA_01.xtc -s DINAMICA_01.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp
#
# g_mmpbsa is part of G R O M A C S:
#
# Giant Rising Ordinary Mutants for A Clerical Setup
#
@ title "APolar solvation energy"
@ xaxis label "Time (ps)"
@ yaxis label "Energy (kJ/mol)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Protein-Surf-ten energy"
@ s1 legend "JZ4-Surf-ten energy"
@ s2 legend "Protein+JZ4-Surf-ten energy"
@ s3 legend "Protein-Press-Vol energy"
@ s4 legend "JZ4-Press-Vol energy"
@ s5 legend "Protein+JZ4-Press-Vol energy"
@ s6 legend "Protein-WCA energy"
@ s7 legend "JZ4-WCA energy"
@ s8 legend "Protein+JZ4-WCA energy"
0.000 223.773 7.571 221.324 0.000 0.000 0.000 0.000 0.000 0.000
2.000 227.264 7.038 224.614 0.000 0.000 0.000 0.000 0.000 0.000
4.000 222.946 7.656 220.365 0.000 0.000 0.000 0.000 0.000 0.000
6.000 229.541 7.250 227.150 0.000 0.000 0.000 0.000 0.000 0.000
8.000 219.315 7.651 216.290 0.000 0.000 0.000 0.000 0.000 0.000
10.000 223.824 7.477 220.583 0.000 0.000 0.000 0.000 0.000 0.000
FILE POLAR.XVG:
# This file was created Sat Nov 8 09:43:38 2014
# by the following command:
# g_mmpbsa -f DINAMICA_01.xtc -s DINAMICA_01.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp
#
# g_mmpbsa is part of G R O M A C S:
#
# Giant Rising Ordinary Mutants for A Clerical Setup
#
@ title "Polar solvation energy"
@ xaxis label "Time (ps)"
@ yaxis label "Energy (kJ/mol)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Protein PB energy"
@ s1 legend "JZ4 PB energy"
@ s2 legend "Protein=JZ4 PB energy"
0.000 -6557.415 -18.088 -6543.196
2.000 -6641.539 -17.782 -6630.493
4.000 -6628.399 -18.070 -6613.423
6.000 -6653.568 -17.157 -6637.181
8.000 -6577.857 -17.451 -6564.387
10.000 -6840.841 -18.140 -6824.860
Please, could you help?
Regards,
Flavio
I install g_mmpbsa from source in a CentosOS 6.5 64bits and also in a Fedora 20 64bits. Both systems have Gromacs 4.5
The tutorial works very fine and was fully completed.
But, when I was trying to use in my sistem (lysozyme inhibitor system in a cubic box with NaCl 0.15M neutral charges), the calculations not finishes. The program does not finishes properly. The last lines at shell are:
----------------------------------------
CALCULATION #4 (mol2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (1.81 A) for exclusion function
Debye length: 0.889267 A
Current memory usage: 297.746 MB total, 331.000 MB high water
Grid dimensions: 97 x 97 x 129
Grid spacings: 0.497 x 0.505 x 0.457
Grid lengths: 47.710 x 48.480 x 58.440
Grid center: (38.385, 39.670, 38.320)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
0.950 A-radius, 1.000 e-charge, 0.150 M concentration
1.810 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Solving PDE (see io.mc* for details)...
Calculating energy (see io.mc* for details)...
Total electrostatic energy = 6.901516896524E+04 kJ/mol
Fixed charge energy = 69015.2 kJ/mol
Mobile charge energy = 233.268 kJ/mol
Dielectric energy = 49294 kJ/mol
Per-atom energies:
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (mol1) - 2 (mol2) end
Local net energy (PE 0) = -6.601057266615E+03 kJ/mol
Global net ELEC energy = -6.601057266615E+03 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 331.000 MB high water
Thanks for using APBS!
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 1.3
Nathan A. Baker (nathan...@pnl.gov)
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of Washington University in St. Louis nor the names of its
contributors may be used to endorse or promote products derived from this
software without specific prior written permission.
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.
----------------------------------------------------------------------
APBS uses FETK (the Finite Element ToolKit) to solve the
Poisson-Boltzmann equation numerically. FETK is a portable collection
of finite element modeling class libraries developed by the Michael Holst
research group and written in an object-oriented form of C. FEtk is
designed to solve general coupled systems of nonlinear partial differential
equations using adaptive finite element methods, inexact Newton methods,
and algebraic multilevel methods. More information about FEtk may be found
at <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2014 at 14:56:24
Parsing input file pw8DCiRA.in...
NOsh: Deprecated use of ION keyword! Use key-value pairs
NOsh: Deprecated use of ION keyword! Use key-value pairs
I understand "NOsh: Deprecated use of ION keyword! Use key-value pairs" is just a warning, but the program are at this stage more than 24 hours in a quad-core machine.
At the biegining of calculations all processors was used, but in this last stage, only one processor are running for more than 24 hours.
The tutorial was finished in less than 10 minuts.
The output files apolar.xvg and polar.xvg contains only part of the 51 frames (0.1 ns):
APOLAR.XVG
# This file was created Sat Nov 8 09:43:38 2014
# by the following command:
# g_mmpbsa -f DINAMICA_01.xtc -s DINAMICA_01.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp
#
# g_mmpbsa is part of G R O M A C S:
#
# Giant Rising Ordinary Mutants for A Clerical Setup
#
@ title "APolar solvation energy"
@ xaxis label "Time (ps)"
@ yaxis label "Energy (kJ/mol)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Protein-Surf-ten energy"
@ s1 legend "JZ4-Surf-ten energy"
@ s2 legend "Protein+JZ4-Surf-ten energy"
@ s3 legend "Protein-Press-Vol energy"
@ s4 legend "JZ4-Press-Vol energy"
@ s5 legend "Protein+JZ4-Press-Vol energy"
@ s6 legend "Protein-WCA energy"
@ s7 legend "JZ4-WCA energy"
@ s8 legend "Protein+JZ4-WCA energy"
0.000 223.773 7.571 221.324 0.000 0.000 0.000 0.000 0.000 0.000
2.000 227.264 7.038 224.614 0.000 0.000 0.000 0.000 0.000 0.000
4.000 222.946 7.656 220.365 0.000 0.000 0.000 0.000 0.000 0.000
6.000 229.541 7.250 227.150 0.000 0.000 0.000 0.000 0.000 0.000
8.000 219.315 7.651 216.290 0.000 0.000 0.000 0.000 0.000 0.000
10.000 223.824 7.477 220.583 0.000 0.000 0.000 0.000 0.000 0.000
FILE POLAR.XVG:
# This file was created Sat Nov 8 09:43:38 2014
# by the following command:
# g_mmpbsa -f DINAMICA_01.xtc -s DINAMICA_01.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp
#
# g_mmpbsa is part of G R O M A C S:
#
# Giant Rising Ordinary Mutants for A Clerical Setup
#
@ title "Polar solvation energy"
@ xaxis label "Time (ps)"
@ yaxis label "Energy (kJ/mol)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Protein PB energy"
@ s1 legend "JZ4 PB energy"
@ s2 legend "Protein=JZ4 PB energy"
0.000 -6557.415 -18.088 -6543.196
2.000 -6641.539 -17.782 -6630.493
4.000 -6628.399 -18.070 -6613.423
6.000 -6653.568 -17.157 -6637.181
8.000 -6577.857 -17.451 -6564.387
10.000 -6840.841 -18.140 -6824.860
Please, could you help?
Regards,
Flavio
g_mmpbsa Mailing List
Nov 9, 2014, 11:47:38 AM11/9/14
to g_mm...@googlegroups.com
From the above information, it is very difficult to trace the problem. Please give us more information. What is in the "io.mc" file? Could you please upload p*.in and p*.pqr file. Have you visualized the pqr file in VMD/Pymol to check the structure. If you have apbs installed, use following command to check whether both .in and .pqr file is accepted directly by apbs program: >apbs p*.in
Flavio Seixas
Nov 9, 2014, 2:48:22 PM11/9/14
to g_mm...@googlegroups.com
Hi, thank you for help.
A little more
information: I run the MD simulation using GROMOS96.1 force field,
which gives only Polar and Aromatic hydrogens for protein and ligand.
Could it affect the results?
I run the p* files from shell as you suggested (see below).
Aparently the p*.in is accepted by apbs, but p*.pqr is not. It may be the reason of the problem.[flavios@dhcppc1 mmpbsa]$ apbs pw8DCiRA.in
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Aug 3 2013 at 01:38:13
Parsing input file pw8DCiRA.in...
NOsh: Deprecated use of ION keyword! Use key-value pairs
NOsh: Deprecated use of ION keyword! Use key-value pairs
[flavios@dhcppc1 mmpbsa]$ apbs pw8DCiRA.pqr
LAST LINES:
--------------------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Aug 3 2013 at 01:38:13
Parsing input file pw8DCiRA.pqr...
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 1!
NOsh_parseInput: Ignoring undefined keyword C4!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 39.410!
NOsh_parseInput: Ignoring undefined keyword 31.670!
NOsh_parseInput: Ignoring undefined keyword 50.450!
NOsh_parseInput: Ignoring undefined keyword 0.000!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 2!
NOsh_parseInput: Ignoring undefined keyword C14!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 39.340!
NOsh_parseInput: Ignoring undefined keyword 31.050!
NOsh_parseInput: Ignoring undefined keyword 49.050!
NOsh_parseInput: Ignoring undefined keyword 0.000!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 3!
NOsh_parseInput: Ignoring undefined keyword C13!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.040!
NOsh_parseInput: Ignoring undefined keyword 31.340!
NOsh_parseInput: Ignoring undefined keyword 48.290!
NOsh_parseInput: Ignoring undefined keyword 0.000!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 4!
NOsh_parseInput: Ignoring undefined keyword C12!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.060!
NOsh_parseInput: Ignoring undefined keyword 30.530!
NOsh_parseInput: Ignoring undefined keyword 47.160!
NOsh_parseInput: Ignoring undefined keyword 0.000!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 5!
NOsh_parseInput: Ignoring undefined keyword C11!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 37.290!
NOsh_parseInput: Ignoring undefined keyword 29.370!
NOsh_parseInput: Ignoring undefined keyword 47.230!
NOsh_parseInput: Ignoring undefined keyword -0.100!
NOsh_parseInput: Ignoring undefined keyword 1.770!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 6!
NOsh_parseInput: Ignoring undefined keyword H11!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 36.960!
NOsh_parseInput: Ignoring undefined keyword 28.950!
NOsh_parseInput: Ignoring undefined keyword 48.180!
NOsh_parseInput: Ignoring undefined keyword 0.100!
NOsh_parseInput: Ignoring undefined keyword 1.200!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 7!
NOsh_parseInput: Ignoring undefined keyword C7!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 37.100!
NOsh_parseInput: Ignoring undefined keyword 28.570!
NOsh_parseInput: Ignoring undefined keyword 46.110!
NOsh_parseInput: Ignoring undefined keyword -0.100!
NOsh_parseInput: Ignoring undefined keyword 1.770!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 8!
NOsh_parseInput: Ignoring undefined keyword H7!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 36.760!
NOsh_parseInput: Ignoring undefined keyword 27.540!
NOsh_parseInput: Ignoring undefined keyword 46.190!
NOsh_parseInput: Ignoring undefined keyword 0.100!
NOsh_parseInput: Ignoring undefined keyword 1.200!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 9!
NOsh_parseInput: Ignoring undefined keyword C8!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 37.600!
NOsh_parseInput: Ignoring undefined keyword 28.960!
NOsh_parseInput: Ignoring undefined keyword 44.870!
NOsh_parseInput: Ignoring undefined keyword -0.100!
NOsh_parseInput: Ignoring undefined keyword 1.770!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 10!
NOsh_parseInput: Ignoring undefined keyword H8!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 37.870!
NOsh_parseInput: Ignoring undefined keyword 28.160!
NOsh_parseInput: Ignoring undefined keyword 44.190!
NOsh_parseInput: Ignoring undefined keyword 0.100!
NOsh_parseInput: Ignoring undefined keyword 1.200!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 11!
NOsh_parseInput: Ignoring undefined keyword C9!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.340!
NOsh_parseInput: Ignoring undefined keyword 30.140!
NOsh_parseInput: Ignoring undefined keyword 44.790!
NOsh_parseInput: Ignoring undefined keyword -0.100!
NOsh_parseInput: Ignoring undefined keyword 1.770!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 12!
NOsh_parseInput: Ignoring undefined keyword H9!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.830!
NOsh_parseInput: Ignoring undefined keyword 30.430!
NOsh_parseInput: Ignoring undefined keyword 43.860!
NOsh_parseInput: Ignoring undefined keyword 0.100!
NOsh_parseInput: Ignoring undefined keyword 1.200!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 13!
NOsh_parseInput: Ignoring undefined keyword C10!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.590!
NOsh_parseInput: Ignoring undefined keyword 30.890!
NOsh_parseInput: Ignoring undefined keyword 45.930!
NOsh_parseInput: Ignoring undefined keyword 0.150!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 14!
NOsh_parseInput: Ignoring undefined keyword OAB!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 39.320!
NOsh_parseInput: Ignoring undefined keyword 32.030!
NOsh_parseInput: Ignoring undefined keyword 45.780!
NOsh_parseInput: Ignoring undefined keyword -0.548!
NOsh_parseInput: Ignoring undefined keyword 1.520!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 15!
NOsh_parseInput: Ignoring undefined keyword HAB!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 39.290!
NOsh_parseInput: Ignoring undefined keyword 32.490!
NOsh_parseInput: Ignoring undefined keyword 46.670!
NOsh_parseInput: Ignoring undefined keyword 0.398!
NOsh_parseInput: Ignoring undefined keyword 1.200!
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
Parsed input file.
Got paths for 0 molecules
You didn't specify any molecules (correctly)!
Bailing out!
Error reading molecules!
[flavios@dhcppc1 mmpbsa]$
Parsing input file pw8DCiRA.pqr...
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 1!
NOsh_parseInput: Ignoring undefined keyword C4!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 39.410!
NOsh_parseInput: Ignoring undefined keyword 31.670!
NOsh_parseInput: Ignoring undefined keyword 50.450!
NOsh_parseInput: Ignoring undefined keyword 0.000!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 2!
NOsh_parseInput: Ignoring undefined keyword C14!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 39.340!
NOsh_parseInput: Ignoring undefined keyword 31.050!
NOsh_parseInput: Ignoring undefined keyword 49.050!
NOsh_parseInput: Ignoring undefined keyword 0.000!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 3!
NOsh_parseInput: Ignoring undefined keyword C13!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.040!
NOsh_parseInput: Ignoring undefined keyword 31.340!
NOsh_parseInput: Ignoring undefined keyword 48.290!
NOsh_parseInput: Ignoring undefined keyword 0.000!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 4!
NOsh_parseInput: Ignoring undefined keyword C12!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.060!
NOsh_parseInput: Ignoring undefined keyword 30.530!
NOsh_parseInput: Ignoring undefined keyword 47.160!
NOsh_parseInput: Ignoring undefined keyword 0.000!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 5!
NOsh_parseInput: Ignoring undefined keyword C11!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 37.290!
NOsh_parseInput: Ignoring undefined keyword 29.370!
NOsh_parseInput: Ignoring undefined keyword 47.230!
NOsh_parseInput: Ignoring undefined keyword -0.100!
NOsh_parseInput: Ignoring undefined keyword 1.770!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 6!
NOsh_parseInput: Ignoring undefined keyword H11!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 36.960!
NOsh_parseInput: Ignoring undefined keyword 28.950!
NOsh_parseInput: Ignoring undefined keyword 48.180!
NOsh_parseInput: Ignoring undefined keyword 0.100!
NOsh_parseInput: Ignoring undefined keyword 1.200!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 7!
NOsh_parseInput: Ignoring undefined keyword C7!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 37.100!
NOsh_parseInput: Ignoring undefined keyword 28.570!
NOsh_parseInput: Ignoring undefined keyword 46.110!
NOsh_parseInput: Ignoring undefined keyword -0.100!
NOsh_parseInput: Ignoring undefined keyword 1.770!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 8!
NOsh_parseInput: Ignoring undefined keyword H7!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 36.760!
NOsh_parseInput: Ignoring undefined keyword 27.540!
NOsh_parseInput: Ignoring undefined keyword 46.190!
NOsh_parseInput: Ignoring undefined keyword 0.100!
NOsh_parseInput: Ignoring undefined keyword 1.200!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 9!
NOsh_parseInput: Ignoring undefined keyword C8!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 37.600!
NOsh_parseInput: Ignoring undefined keyword 28.960!
NOsh_parseInput: Ignoring undefined keyword 44.870!
NOsh_parseInput: Ignoring undefined keyword -0.100!
NOsh_parseInput: Ignoring undefined keyword 1.770!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 10!
NOsh_parseInput: Ignoring undefined keyword H8!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 37.870!
NOsh_parseInput: Ignoring undefined keyword 28.160!
NOsh_parseInput: Ignoring undefined keyword 44.190!
NOsh_parseInput: Ignoring undefined keyword 0.100!
NOsh_parseInput: Ignoring undefined keyword 1.200!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 11!
NOsh_parseInput: Ignoring undefined keyword C9!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.340!
NOsh_parseInput: Ignoring undefined keyword 30.140!
NOsh_parseInput: Ignoring undefined keyword 44.790!
NOsh_parseInput: Ignoring undefined keyword -0.100!
NOsh_parseInput: Ignoring undefined keyword 1.770!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 12!
NOsh_parseInput: Ignoring undefined keyword H9!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.830!
NOsh_parseInput: Ignoring undefined keyword 30.430!
NOsh_parseInput: Ignoring undefined keyword 43.860!
NOsh_parseInput: Ignoring undefined keyword 0.100!
NOsh_parseInput: Ignoring undefined keyword 1.200!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 13!
NOsh_parseInput: Ignoring undefined keyword C10!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 38.590!
NOsh_parseInput: Ignoring undefined keyword 30.890!
NOsh_parseInput: Ignoring undefined keyword 45.930!
NOsh_parseInput: Ignoring undefined keyword 0.150!
NOsh_parseInput: Ignoring undefined keyword 1.700!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 14!
NOsh_parseInput: Ignoring undefined keyword OAB!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 39.320!
NOsh_parseInput: Ignoring undefined keyword 32.030!
NOsh_parseInput: Ignoring undefined keyword 45.780!
NOsh_parseInput: Ignoring undefined keyword -0.548!
NOsh_parseInput: Ignoring undefined keyword 1.520!
NOsh_parseInput: Ignoring undefined keyword ATOM!
NOsh_parseInput: Ignoring undefined keyword 15!
NOsh_parseInput: Ignoring undefined keyword HAB!
NOsh_parseInput: Ignoring undefined keyword JZ4!
NOsh_parseInput: Ignoring undefined keyword 164!
NOsh_parseInput: Ignoring undefined keyword 39.290!
NOsh_parseInput: Ignoring undefined keyword 32.490!
NOsh_parseInput: Ignoring undefined keyword 46.670!
NOsh_parseInput: Ignoring undefined keyword 0.398!
NOsh_parseInput: Ignoring undefined keyword 1.200!
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
Parsed input file.
Got paths for 0 molecules
You didn't specify any molecules (correctly)!
Bailing out!
Error reading molecules!
[flavios@dhcppc1 mmpbsa]$
g_mmpbsa Mailing List
Nov 9, 2014, 4:13:10 PM11/9/14
to g_mm...@googlegroups.com
Hi,
We found a bug during the calculation of grid points, which only happens with very small molecule such as the above ligand. We have corrected it. Please, find the attached "psize.c" file. Replace this file with previous one and recompile g_mmpbsa. Try again this calculation and please tell us, how it goes.
A little more information: I run the MD simulation using GROMOS96.1 force field, which gives only Polar and Aromatic hydrogens for protein and ligand. Could it affect the results?
We have not tested the prediction of g_mmpbsa with this force-field. You may have to look up literature.
Thank you for helping us to identifying a bug.
Flavio Seixas
Nov 11, 2014, 5:36:29 PM11/11/14
to g_mm...@googlegroups.com
Hi!
I follow your instructions and the program finishes normally.
It is running very fine now.
Thank you for your help.
Regards,
Flavio
I follow your instructions and the program finishes normally.
It is running very fine now.
Thank you for your help.
Regards,
Flavio
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