rashmikumari/g_mmpbsa

MM-PBSA method for GROMACS. For full description, please visit homepage:

g_mmpbsa's Issues

Positive binding energy

Hi, I am following the tutorial on my simulation (protein ligand) with charmm force field.
I am getting positive binding energy

SUMMARY

van der Waal energy = -160.471 +/- 6.754 kJ/mol

Electrostattic energy = -38.688 +/- 7.770 kJ/mol

Polar solvation energy = 279.916 +/- 14.554 kJ/mol

SASA energy = -22.288 +/- 0.910 kJ/mol

SAV energy = 0.000 +/- 0.000 kJ/mol

WCA energy = 0.000 +/- 0.000 kJ/mol

Binding energy = 58.469 +/- 11.848 kJ/mol

===============
END

Any idea how to solve this?
Thanks
Eldhose

mg-type flag ignored

Hello,

I don't know if this page is monitored anymore, but the mailing list seems to be sparingly used at this point. It seems that flagging the mg-type has no effect in the precompiled binaries, and the type appears to be automatically selected based on the system size. My system is large, and while the receptor and ligand complete successfully for the polar calculation, the calculation for the complex fails. Upon inspection of the input file generated along side the pqr file, "mg-para" has been flagged as opposed to "mg-auto", causing a failure. As a test, I set mg-type = mg-para in the input mdp file, and obtained the same result. This would imply that the flag is ignored, since no output should have happened (it should have failed on the first calculation).

Thank you in advance; this is a very useful software for my smaller systems!

Will Martin

MmPbSaDecomp indentation (MacOS)

MmPbSaDecomp.py has the following issue:
python ./tools/MmPbSaDecomp.py -bs -nbs 2000 -m contrib_MM.dat -p contrib_pol.dat -a contrib_apol.dat
File "./tools/MmPbSaDecomp.py", line 133
args = parser.parse_args()
^
IndentationError: unexpected indent

I apologize if I am missing something trivial.

can we use topol.top instead of topol.tpr

In my simulation with, it generated topol.top then, how I can do mmpbsa analysis.

【Help】run error

[Question] Is ARM64 a supported architecture?

Hello,

I’d like to ask whether g_mmpbsa is supported on Linux/Mac ARM64 systems ?
Any concerns ?
Any positive/negative experience ?

Thank you!

incorporate all CPU cores

Hi dear friends. how we can incorporate all CPU cores in the g_mmpbsa computation?

energy2bfac: Illegal instruction

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 (-:                            

           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

how to generate topology-parameter (tpr), atom-index (ndx), and trajectory (xtc) files

apbs installation

Hello, I follow the steps below for APBS-1.4:

# Download using git from GitHub repository
git clone -b 1.4.1-binary-release --single-branch https://github.com/Electrostatics/apbs-pdb2pqr
cd apbs-pdb2pqr
cd apbs
cd build
sh cleanup.sh
# Installation
cmake -DCMAKE_INSTALL_PREFIX=/opt/apbs -DENABLE_BEM=off -DENABLE_iAPBS=on ..
make
sudo make install

After I enter the command below:

cmake -DCMAKE_INSTALL_PREFIX=/opt/apbs -DENABLE_BEM=off -DENABLE_iAPBS=on ..

The error in the picture occurs. I also tried apbs 1.3 and 1.5. Any help would be appreciated.
Thanks

Containerised deployment option

Hi,

As part of a project for the UK Biomolecular simulation community we are developing a library of containerised popular applications, and would like to include g_mmpbsa in this. It's called pinda and you can see more here. In essence, it's a bit like Conda or pip, but based on Docker/Singularity containers.

If you would like to know more, please get in touch.

Regards, Charlie

translate g_mmpbsa1.1.0 to arm

My configuration adopts:./configure CC=clang CXX=clang++ F77=flang --with-gmx-include=/path/to/gromacs/include --with-gmx-lib=/path/to/gromacs/lib --with-apbs=/path/to/apbs-1.3-source --with-apbs-lib=/path/to/apbs/lib --build=arm .
When I execute make, an error is reported：

thank you very much！ @RashmiKumari

Update to use Gromacs 2020.2 and APBS 3.0

Hi! any plans to update g_mmpbsa to use Gromacs 2020.2 and APBS 3.0?

Best

Why is the at_count variable for atom count being compared as

I am getting this error below using (sounds like I need to be a mind reader to understand this one 😵‍💫 ):

Fatal error:
Number of atoms in selected index (31) does not match with number of atoms (1) in APBS output.

Very confused by this code in https://github.com/RashmiKumari/g_mmpbsa/blob/master/src/GMX50/extrn_apbs.c
Won't the at_count always be1? How is this code supposed to work???? I used this input for testing https://github.com/RashmiKumari/g_mmpbsa/blob/master/test/polar_orig/mmpbsa.mdp. Beyond frustrated now...

/* Memory allocation for atom energy */
	if (AtomEnergy != NULL)	{
		snew(atEnergy1, 1);
		snew(atEnergy2, 1);
		at_count = 1;
	}

...
if ((AtomEnergy != NULL) && (at_count-1 != isize) )	{
					gmx_fatal(FARGS,"Number of atoms in selected index (%d) does not match with number of atoms (%d) in APBS output. \n", isize, at_count);
				}

Running g_mmpbsa in background

Hello,

I want to know how to run g_mmpbsa in the background.

I have all the files in a server that I access using SSH. As the calculations don't give an immediate result, if I close the connection, the calculation is stopped.

If I add the & at the end, after selected the groups to calculate the binding energy, the program return an error and stop the calculation.

Is there a way to pass the selected groups to calculate the binding energy in the command line?

Thanks in advance

builtins module

Hi All,

I executed the "python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg" command. But, I got the following error:

Traceback (most recent call last):
File "MmPbSaStat.py", line 39, in
from builtins import range
ImportError: No module named builtins

Can you please help me figure this out?

Regards,
Mohammad

Segmentation fault (core dumped)

When I run ''g_mmpbsa -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../polar.mdp -nomme -pbsa -decomp'', It reports me with Segmentation fault (core dumped), how to solve it?

where is manual of mutate_traj_tpr.py

in g_mmpbsa ,there is not manual of mutate_traj_tpr.py, so we do not kown how to utilize it. can manual of mutate_traj_tpr.py be added?

Library file 'residuetypes.dat' not found

Running tutorial files

energy2bfac -s 1EBZ_pbc_corrected.tpr -i energyMapIn.dat

---

Program: energy2bfac, VERSION 5.1.2
Source file: src/gromacs/utility/datafilefinder.cpp (line 210)
Function: std::string gmx::DataFileFinder::findFile(const gmx::DataFileOptions&) const

System I/O error:
Library file 'residuetypes.dat' not found in current dir nor in the default
directories.
The following paths were searched:
/mnt/c/Users/dines/Documents/MD/g_mmpbsa/tutorial/1EBZ (current dir)

/home/rajendra/software/gromacs_install/gmx512_static_woTNG/share/gromacs/top
(default)
You can set additional directories to search with the GMXLIB path variable.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

---

VdW/Elec for Protein and Ligand is 0 in Vacuum MM energy - in the tutorial

I downloaded your tutorial from here: https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_binding_energy.html

Regardless of whether MM is computed separately or together with PBSA, these terms are always 0. Here is the energy_MM.xvg attached: mm.zip

My GMXLIB points at my 5.1.4 gromacs top directory but this has not changed anything.

At the same time, the python script MmPbSaStat.py uses the columns:
Energy = mmEn[5][i] - (mmEn[1][i] + mmEn[3][i])
Vdw.append(Energy)

The original MMPBSA shows that there is a different potential energy betweenthe protein+ligand and the complex.

Am I doing something wrong or is this a very serious issue?

arm transplantion

Have you tested the transplant of arm framework? Recently, I encountered a lot of problems in porting the arm framework. Please inform me

RAM memory problems

I have a large dataset and I've just noticed that my process is killed.

My dmesg says that the process took over 20GB:

Killed process 14036 (g_mmpbsa) total-vm:26639468kB

I presume this means that the entire simulation is loaded to the RAM memory. If that's true, is this really necessary? Thanks

Can't reproduce the full output of the tutorial

Hey! I've downloaded the tutorial and run the bash inside it and it's not generating certain output that comes with the tutorial.

Anyone knows something?

Thank you!

【Help】Installation failure

What should I do if the following header files are not recognized when using mpi installation？

Looking for update version for gromacs 2020.1

g_mmpbsa is working fine on gromacs 2018 but not work on 2020.1.
Could you tell me how I can use g_mmpbsa on gromacs 2020.1 version.
Thank you.

error in LIG PB energy"

Hello,
I am trying to do MM_PBSA calculations of Protein-Ligand complex. I am getting an error in polar.xvg; there is a text "nan" instead of numericals in the column for Lig PB energy. Please let me know what is the error. The same error "nan" was observed in Electrostatic energy between Protein-LIgand and also in Binding energy of Ligand calculated at later stage. Kindly let me know what should be done.

Unspecified input error

I am attempting to run g_mmpbsa on a GROMACS MD simulation. I ran the command g_mmpbsa -f md_0_1.xtc -s md_0_1.tpr -n mmpbsa.ndx -i mmpbsa.mdp -pdie 2 -pbsa -decomp. I then selected my protein and ligand groups defined in my index file groups 18 and 19, respectively. The program seemed to be running through each frame of the MD simulation and generating this same error message at each step. It seems that I have incorrectly formated input data but I am unsure which of my files is the problem here and why. I am using the mdp file parameters provided in the github tutorial https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_binding_energy.html under the tests/wca_orig folder. Could you help me understand my error? Below is the error output message.

This executable compiled on May 13 2020 at 16:26:56

Parsing input file APpiKTtoFA.in...
Parsed input file.
Reading parameter data from piKTtoF_param.dat.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
Got paths for 1 molecules

WARNING!! Radius/charge information from PQR file piKTtoFA.pqr
will be replaced with data from parameter file (piKTtoF_param.dat)!
Reading PQR-format atom data from piKTtoFA.pqr.
Vparam_getAtomData: unable to find atom 'O1', res 'TRP'
Valist_readPDB: Couldn't find parameters for atom = O1, residue = TRP
Error reading molecules!
Killed

builtins for MmPbSaStat.py

May I know where to get the builtins module so I can run the calculation for average binding energy?

Traceback (most recent call last):
File "../mmpbsa/MmPbSaStat.py", line 39, in
from builtins import range
ImportError: No module named builtins

Install g_mmpbsa error

I install g_mmpbsa in linux system, but I encounter an error, as following:
'''
-- checking for module 'libgromacs'
-- package 'libgromacs' not found
-- Could NOT find GROMACS (missing: GROMACS_LIBRARY)
-- Continue checking for other Gromacs version library file
-- checking for module 'libgmx'
-- package 'libgmx' not found
-- Could NOT find GROMACS (missing: GROMACS_LIBRARY)
CMake Error at src/CMakeLists.txt:72 (message):

Gromacs path is not defined.....

USE:

-DGMX_PATH=/path/to/gromacs
or
export CMAKE_PREFIX_PATH="/path/to/gromacs"

-- Configuring incomplete, errors occurred!
'''
This is my command:
'''cmake -DGMX_PATH=/home/rwshi/soft/gmx465-1/ -DAPBS_INSTALL=//home/dpli/software/apbs -DAPBS_SRC=/home/dp
li/software/apbs-1.3-source -DCMAKE_INSTALL_PREFIX=/home/dpli/software/g_mmpbsa ..'''

g_mmpbsa not compatible with gromacs-2019.x

I get a memory allocation error when .tpr file is coming from a simulation run using gromacs-2019.x
Reading file step7.tpr, VERSION 2019.4 (single precision)
Reading file step7.tpr, VERSION 2019.4 (single precision)

---

Program g_mmpbsa, VERSION 5.1.2
Source code file: /home/rajendra/software/gromacs_source/gromacs-5.1.2/src/gromacs/utility/smalloc.c, line: 182

Fatal error:
Not enough memory. Failed to calloc 1330119044 elements of size 4 for cmap_grid->cmapdata[i].cmap
(called from file /home/rajendra/software/gromacs_source/gromacs-5.1.2/src/gromacs/fileio/tpxio.c, line 2786)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

: Cannot allocate memory

That is problematic as it's starting to be hard to find systems with such an old version of gromacs, also, I am unsure about how well will work the regeneration of the .tpr file with old gromacs using that with all the other files and traj generated with newer gmx

Thanks a lot

RuntimeWarning: invalid value encountered in subtract while running g_mmpbsa

Hi, while running Average Binding Energy Calculation I'm getting "RuntimeWarning: invalid value encountered in subtract
x = asanyarray(arr - arrmean)". How to solve this error?

Pls help, can not find the '`configure' shell script to install GMM..?

Hi,

I have cloned the source code for g_mmpbsa from GitHub but can not find the `configure' shell script to install GMM..?

Please help!

Thanks in advance,
Ash

Is there something wrong in the tutorial files?

The file link:http://rashmikumari.github.io/g_mmpbsa/tutorial.tar.gz
~/tutorials/pbsa.mdp
Line 90, sasaconst = 3.84982
It should be 'sasaconst = 3.84928'
as you have refered in the article,
Wang, Wei, and Peter A. Kollman. "Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model." Journal of molecular biology 303.4 (2000): 567-582.

Standard error or precesion in energies is higher than their energies-Reg

Madam/Sir,
It is brought to your note that while performing gmmpbsa after final mdrun (100 ns), I am getting higher standard values than their energies. I never had such an anomaly earlier while performing the Protein-Ligand gmmpbsa. I am herewith enclosed my summary-energy.dat file for your perusal and suggestion. Further to decrease the precision several short gaps (10ns) with more frames (1200) are also calculated. Pls correct me.

#Complex Number: 1

SUMMARY

van der Waal energy = -0.966 +/- 4.489 kJ/mol

Electrostattic energy = -0.946 +/- 6.339 kJ/mol

Polar solvation energy = 0.466 +/- 40.830 kJ/mol

SASA energy = -0.108 +/- 1.815 kJ/mol

SAV energy = 0.000 +/- 0.000 kJ/mol

WCA energy = 0.000 +/- 0.000 kJ/mol

Binding energy = -1.554 +/- 39.725 kJ/mol

===============
END

Thanking You
Dr Md Nayeem

Problem compiling with gromacs-5.1.2

Hello!

Firstly thank you for the effort of developing the tool, it's awesome!

I first tested the version from the binary download - which works perfectly, I then wanted to compile (to get a better performance and so on and got a an error during configuration - saying that the gromacs libgmx was not found.

I use gromacs-5.1.2 installed to its default location (/usr/local/gromacs), during g_mmpbsa configuration I set the PATH_TO_GROMACS flag (however it actually writes) to my gromacs install location; I also tried providing the path to the actual libgmx* files (in /usr/lib) in addition to the first path, i tried exporting the relevant paths (export <RELEVANT_PATHS> (in accordance to the installation guide you provide). Still I'm getting the same error.

Have you faced this kind of issue before, did you already start working on a solution?

Apparently the configuration (the cmake scripts) search for a libgmx folder, which is not present in gmx-5.1.2 - does this conclusion make sense?

Do you have any ideas, how to fix it? What does it actually need from it? Can I feed him the directory in another fashion (within the cmake) or would I have to rewrite large sections?

Thanks again!
Sincerely,

tomaz

g_mmpbsa and gromacs 2020.04

during calculation of binding energy by g_mmpbsa for gromacs 2020.04 i get below error. what's solution for this error?

g_mmpbsa installation error

During g_mmpbsa installation I am getting CMake error as shown below....

CMake Error: The source directory "/path/to/g_mmpbsa" does not appear to contain CMakeLists.txt.
Specify --help for usage, or press the help button on the CMake GUI.

and the command that I used
cmake -DGMX_PATH=/usr/local/gromacs
- DAPBS_INSTALL=/path/to/apbs/
- DAPBS_SRC=/path/to/apbs/src
- DCMAKE_INSTALL_PREFIX=/usr/local/g_mmpbsa
..

Does anybody came across similar error and found the way to resolve.
I will be thankful for the information regarding the issue.

-pbsa should be switched on by default

If I understand right, the main reason behind the existence of this package is the PBSA calculation. I've used your software naively just to realise that I only did the MM part later when I read the paper. But in some way this is very ironic and misleading that you can run software called mmpbsa and it by default only does not do pbsa. I believe this should be by default switched on.

Segmentation fault (core dumped)

---

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 Apr 19 2016 at 23:49:16

Parsing input file pzI1YbtA.in...
calculate_energy.sh: line 6: 5604 Done echo 1 13
5605 Segmentation fault (core dumped) | g_mmpbsa -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../polar.mdp -nomme -pbsa -decomp
:-) GROMACS - g_mmpbsa, VERSION 5.1.2 (-:

                        GROMACS is written by:
 Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   

Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

##################################################################
second steps，Calculation of polar solvation energy

get error“Segmentation fault (core dumped)” ，others is OK。

python Mmpbsastat.py

Facing an error
NameError: name 'false' is not defined. Did you mean: 'False'?

builtins in line 39 & 40

I wanted to calculate the binding energy of a protein-ligand complex by MmPbSaStat.py and the contribution of residues to the binding energy by MmPbSaDecomp.py; however, I couldn't because of the word builtins in line 39 & 40 in both code. When I put # before these two line I was able to run and calculate the energy. Could you please tell me if the line 39 & 40 are very important to obtain the accurate value or they do not have any effect on the results?