I am trying to use your energy2bfac script. I am able to generate all the input data files, but end up with an illegal instruction error. I suspect that I am not properly producing the input file. I have tried a number of options, including the PBC-corrected output used in g_mmpbsa, the md.tpr file from the simulation, and the md.gro that is the default output. energyMapIn.dat looks appropriate. Would you mind giving a bit more detail on an appropriate input file, or, alternatively, where this might be crashing?
:-) g_mmpbsa (-:
Authors: Rashmi Kumari and Andrew Lynn
Contribution: Rajendra Kumar
Copyright (C) 2013, 2014 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
-s md.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-i energyMapIn.dat Input Generic data file
-n index.ndx Input, Opt! Index file
-c complex.pdb Output, Opt. Protein data bank file
-s1 subunit_1.pdb Output, Opt. Protein data bank file
-s2 subunit_2.pdb Output, Opt. Protein data bank 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
Hello,
I am trying to use your energy2bfac script. I am able to generate all the input data files, but end up with an illegal instruction error. I suspect that I am not properly producing the input file. I have tried a number of options, including the PBC-corrected output used in g_mmpbsa, the md.tpr file from the simulation, and the md.gro that is the default output. energyMapIn.dat looks appropriate. Would you mind giving a bit more detail on an appropriate input file, or, alternatively, where this might be crashing?
Thanks! Adrian
$ energy2bfac -s md.tpr -i energyMapIn.dat -n index.ndx
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.
Option Filename Type Description
-s md.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -i energyMapIn.dat Input Generic data file -n index.ndx Input, Opt! Index file -c complex.pdb Output, Opt. Protein data bank file -s1 subunit_1.pdb Output, Opt. Protein data bank file -s2 subunit_2.pdb Output, Opt. Protein data bank 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