@Ubunting-Biochemist I think forging ahead is great! Could you do all of what you did again, and send me the output at keith@pnnl.gov?
@Ubunting-Biochemist maybe the easiest way is to just copy the stuff from the terminal window and save it to a file. The other way would be to redirect it to a file. So, something like: "command >> output.txt", where command would be "cmake ..." and "make", etc. The >> means to append the output to the file, rather than overwrite it each time.
Hi! I am trying to install APBS on mac OS X El capitan. I followed instructions http://www.poissonboltzmann.org/docs/apbs-installation/ I opened .dmg file and dragged the app to applications. After that, when I ran the app, it opens a terminal and shows PATH=$PATH:
DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:
dirname '/Applications/APBS.app/Contents/MacOS/apbs_term'DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:
dirname '/Applications/APBS.app/Contents/MacOS/apbs_term'/../Frameworks
what should i do next?
Hi @ladanse! I'm sorry that you've hit this problem. We have an issue open for that problem: Electrostatics/apbs-pdb2pqr#450. There is a Solution section where I outline one way to fix it. There is also a more permanent solution in the comment I made on August 29. Finally, we are on the verge of releasing APBS v 1.5 where this problem is finally dealt with. Thanks!
@ladanse also, once you've made the necessary changes outlined in issue 450, to actually run APBS you just type: "apbs " followed by the name of the input file you wish to process. Documentation and examples are available at http://www.poissonboltzmann.org.
Hi guys, I'm attempting to compile CHARMM with iAPBS support, but I'm using a newer version of charmm than is available in the patches -- I'm using c40b1, and the latest patch is c35b2. I've tweaked the makefile using the makefile patch as my guide, and have gotten CHARMM to compile with APBS support, but when I attempt to run one of the example files, I get a segmentation fault.
My APBS version is the source of the 1.5 release on Github (Electrostatics/apbs-pdb2pqr@aa35394) and I compiled using these cmake flags:
cmake -DBUILD_TOOLS=OFF -DENABLE_PYTHON=OFF -DENABLE_OPENMP=OFF -DENABLE_iAPBS=ON -DBUILD_WRAPPER=ON -DENABLE_MPI=OFF ..
I'm using Debian 8.7, and my
uname -a is Linux 018dc623c045 4.9.13-moby #1 SMP Sat Mar 25 02:48:44 UTC 2017 x86_64 GNU/Linux
I've done a little big more digging and debugging, and I've found that there were some issues with the CHARMM source that were causing some issues within APBS/iAPBS driver. However, now, when running an APBS task, I get the following warning from fortran:
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL. When I ran gdb and did some debugging, I found that it was caused by APBS. The best digging I could do is that it is caused somewhere during the initAPOL routine in APBS, closely after Destroying multigrid structures. is logged.
Here's part of the backtrace:
Vpmg_ibForce: No force for zero ionic strength!
mgF tot 17 -4.403e+01 -4.021e+01 -7.123e+01
mgF qf 17 -4.403e+01 -4.021e+01 -7.123e+01
mgF ib 17 0.000e+00 0.000e+00 0.000e+00
mgF db 17 -0.000e+00 -0.000e+00 -0.000e+00
Vpmg_ibForce: No force for zero ionic strength!
mgF tot 18 -1.777e+01 -6.556e+00 -1.234e+00
mgF qf 18 -1.834e+01 -8.440e+00 -1.483e+00
mgF ib 18 0.000e+00 0.000e+00 0.000e+00
mgF db 18 5.610e-01 1.883e+00 2.488e-01
Vpmg_ibForce: No force for zero ionic strength!
mgF tot 19 1.835e+00 4.241e+00 -3.509e+00
mgF qf 19 1.835e+00 4.241e+00 -3.509e+00
mgF ib 19 0.000e+00 0.000e+00 0.000e+00
mgF db 19 -0.000e+00 -0.000e+00 -0.000e+00
Vpmg_ibForce: No force for zero ionic strength!
mgF tot 20 4.713e+00 2.707e-01 3.614e+00
mgF qf 20 4.713e+00 2.707e-01 3.614e+00
mgF ib 20 0.000e+00 0.000e+00 0.000e+00
mgF db 20 -0.000e+00 -0.000e+00 -0.000e+00
Vpmg_ibForce: No force for zero ionic strength!
mgF tot 21 4.481e+00 -4.705e+00 2.504e+00
mgF qf 21 4.481e+00 -4.705e+00 2.504e+00
mgF ib 21 0.000e+00 0.000e+00 0.000e+00
mgF db 21 -0.000e+00 -0.000e+00 -0.000e+00
Destroying multigrid structures.
Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Backtrace for this error:
#0 0x7EFEB284C407
#1 0x7EFEB284CA1E
#2 0x7EFEB1D690DF
#3 0x12A8062 in initAPOL
#4 0x1294B63 in apbsdrv_
#5 0x9E4099 in __iapbs_MOD_apbs at apbs.F90:782
#6 0xC69318 in __pbeq_MOD_pbeq0 at pbeq.F90:377
#7 0x405203 in maincomx_ at charmm_main.F90:1116
#8 0x4077F1 in charmm at charmm_main.F90:407
@jo-sm Sorry for the late response. For some reason the notification went to my spam folder. So from the error you described and giving a second look at your CMake build command could you try build APBS as:
cmake -DBUILD_TOOLS=OFF -DENABLE_PYTHON=OFF -DENABLE_OPENMP=OFF -DENABLE_iAPBS=ON -DBUILD_iAPBS_FORTRAN_WRAPPER=ON -DENABLE_MPI=OFF ..Then try again. Hopefully this takes care of it.
Also, I was able to create a set of patches for the iAPBS module for a newer version of CHARMM (c40b1). The most recent patches are from c35, which are maybe 8-9 years old. Would it be possible to merge in these newer patches into the repository, in
apbs/contrib/iapbs/modules/CHARMM/?
@jo-sm could you email me at juan.brandi-lozano@pnnl.gov with the details of what have you done? Thanks!!
I am trying to "translate" some input files from UHBD to APBS and I am running into some problems
In particular, I need to calculate the potential created by a particular atom over all other atomic positions. This particular atom is the only one with a charge while the rest have zero as a charge. Checking on the manual I see there are two ways to write the potentials: one using write pot and the other using write atompot. I assume that what I need is the second form but I still want to know what the difference between them is
One simple question . Suppose the if delta or the electrostatic potential value in .dx file is 5.315313e-01 implies 0.5315 ?
@kozlac You guys need to qualify the answers a little bit better. I mean this in a constructive way. Remember you are not talking to people who may be experts in the field.
@kozlac In regar to my question I finally figured it out. Write pot writes the potential at every point in the grid which is what you mean by domain.
I know APBS is free and all that stuff but I really think you guys need to work on your documentation rather that in moving forward to implement new features. You need more examples and certainly a better description of the keywords. Again, please don't take these comments as as an attack but rather as a comment on what you need to improve.
Hi there I just download the last version and I'm running a simple LPB case with different grid sizes and I would like to register how long does each of this cases take, but I can't find in the documentation how to do this. Any suggestion?
Just in case, I'm running from the terminal passing an input file.
Thanks
Just in case, I'm running from the terminal passing an input file.
Thanks
@ncclementi Depending on what level of detail you want and which system you are using you could use one of the following. If you are using a bash like terminal the bash command time will print the wall, user, and system time it took to run the script/command like so:
$time ./apbs inputFile.in
real 0m0.096s
user 0m0.084s
sys 0m0.008sAlso, if you are running the program locally on your computer APBS outputs the file io.mc which contains a lot of information. Among others the timings of different APBS' procedures. However, you should copy or rename it after each run otherwise ABPS will append the new output to the same file.
Let me know if this helped. Thanks!!
For the record I have 1 processor with 4 cores, using the 1.4.1 version the the input file I'm running runs in all the threads, while in the 1.5 version just in 1. The input file looks like:
read
mol pqr built_parse.pqr
end
# LYSOZYME SOLVATION ENERGY -- SOLVATED STATE
elec name lys-solv
mg-manual
dime 257 161 257
glen 50 40 50
# glen 69.43 61.38 77.82
gcent mol 1
mol 1
lpbe
bcfl mdh
ion charge 1 conc 0.15 radius 2.0
ion charge -1 conc 0.15 radius 2.0
pdie 4.0
sdie 80.00
chgm spl2
srfm mol
srad 1.4
swin 0.3
sdens 50.0
temp 300.00
calcenergy total
calcforce no
end
# LYSOZYME SOLVATION ENERGY -- REFERENCE STATE
elec name lys-ref
mg-manual
dime 257 161 257
glen 50 40 50
# glen 69.43 61.38 77.82
gcent mol 1
mol 1
lpbe
bcfl mdh
ion charge 1 conc 0.00 radius 2.0
ion charge -1 conc 0.00 radius 2.0
pdie 4.0
sdie 4.00
chgm spl2
srfm mol
srad 1.4
swin 0.3
sdens 50.0
temp 300.00
calcenergy total
calcforce no
end
# Lysozyme solvation energy
print elecEnergy lys-solv - lys-ref end
quit
Hello @ncclementi most likely I forgot to update the binary at sourceforge with the one that has multi-thread support. I'll try to get it up by the end of the week. In the mean you can try the one in the Github repo. I'm certain that one was multi-thread enabled.
Hello @Arvindiyer , could you give me a little more information about how you're building the program?
- Are you building on Windows or Unix like system?
- Did you clone the github repo or are you getting the source code from somewhere else?
- From where and what command are you using when calling Cmake?
Like the error says, the apbscfg.h.in is a template file use by CMake to create the abpscgf.h file. Please make sure that the folder and file exist in <abps-top-level>/src/.config/apbscfg.h.in. If not you could try to copy it from the repo, open a text editor paste it and save it as apbscfg.h.in, and put it in the .config folder.
If the folder and file do exist, then it may be that you are calling CMake from a place where it can't reach the /src folder. I usually create a build folder in apbs' top level and build from there:
<apbs-top-level>$ mkdir build1 && cd build1
<apbs-top-level>/build1$ cmake <cmake-build-options> ..
<apbs-top-level>/build1$ makePlease let me know if this helped. Thanks!!
Hello everybody,
I tried to install apbs on my Computer and my Laptop. After unpacking all files, I tried to run apbs in from the bin folder. Two black boxes appear but immediately disappear again. Nothing else happens. Does anybody know what to do to fix this?
Best Stephan