Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    Keith T. Star
    @keith923
    @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?
    Keith T. Star
    @keith923
    I'm sorry to make you do that, but it'll help me see where things are running off the rails if I can see all of the output.
    Ubunting-Biochemist
    @Ubunting-Biochemist
    No problem! Since I am a newbie, can you tell me how I can easily make such an output file? I would guess I just issue a log command of some kind at the beginning of my ssh session?
    Keith T. Star
    @keith923
    @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.
    Ubunting-Biochemist
    @Ubunting-Biochemist
    Ok. I'll send it all to you ASAP! Thanks.
    Juan
    @kozlac
    @Ubunting-Biochemist Have you had any luck? Please let me know if there's any further help could provide. Thanks!
    Ubunting-Biochemist
    @Ubunting-Biochemist
    Not I, but @keith923 is working on looking through the output of my failed compile to see if he can find the problem. Maybe he would appreciate. Second set of eyes. If so I can forward the output to you @kozlac. Thanks!
    Juan
    @kozlac
    That sounds good. You can email it to me at juan.brandi-lozano@pnnl.gov
    ladanse
    @ladanse
    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=$PATH:dirname '/Applications/APBS.app/Contents/MacOS/apbs_term'
    DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:dirname '/Applications/APBS.app/Contents/MacOS/apbs_term'/../Frameworks
    what should i do next?
    Keith T. Star
    @keith923
    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!
    Keith T. Star
    @keith923
    @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.
    ladanse
    @ladanse
    @keith923 I will try to install the latest version. Thanks for your help!!
    Keith T. Star
    @keith923
    @ladanse great! Thanks!
    xl23
    @arrow50311
    Hi when installing APBS from source code it cannot find apbs-pdb2pqr/apbs/externals/fetk/maloc, anyone know where can I download this maloc file?
    Joshua Smock
    @jo-sm
    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 ..
    Juan
    @kozlac
    @jo-sm Have you tried to run the APBS binary by itself? If apbs is the one segfaulting there's some stuff we can look at. If APBS gets to at least initialize there should be a io.txt file. Also, it would be helpful if you could generate a core dump file, what system are you using?
    Joshua Smock
    @jo-sm
    Hey @kozlac, I just ran the APBS binary and it did run, and gave me an io.mc output file. However, charmm uses the iAPBS driver, so it might not produce the same file.
    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
    Joshua Smock
    @jo-sm
    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
    Juan
    @kozlac

    @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.

    Joshua Smock
    @jo-sm
    @kozlac I tried building with the flags you sent me but it still gives me the IEEE_DENORMAL error :/
    Joshua Smock
    @jo-sm
    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/?
    Juan
    @kozlac
    Hello @jo-sm , I have contacted someone who might be able to help us.
    Juan
    @kozlac
    @jo-sm could you email me at juan.brandi-lozano@pnnl.gov with the details of what have you done? Thanks!!
    Joshua Smock
    @jo-sm
    @kozlac Sent you an email :)
    ZacInMA
    @ZacInMA
    Hello
    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
    Priya Moganti
    @Priya_Moganti_twitter
    Hi
    One simple question . Suppose the if delta or the electrostatic potential value in .dx file is 5.315313e-01 implies 0.5315 ?
    Juan
    @kozlac
    @ZacInMA The "write pot" writes the potential over the entire domain while "write atompot" only writes the potential at the atom positions. In your case, I think it is atompot what you want.
    Juan
    @kozlac
    @Priya_Moganti_twitter Yes 5.315313e-01 = 0.5315313 in the opendx format files.
    ZacInMA
    @ZacInMA
    What is the difference between gcent and cgcent?
    @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.
    ZacInMA
    @ZacInMA
    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.
    Nathan Baker
    @sobolevnrm
    @ZacInMA Thank you for your feedback. Are there specific areas where you would like to see the documentation improved?
    Naty Clementi
    @ncclementi
    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
    Juan
    @kozlac

    @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     0m0.008s

    Also, 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!!

    Naty Clementi
    @ncclementi
    @kozlac I'm looking for wall time so I think the bash option is the best.
    Thanks a lot!
    Naty Clementi
    @ncclementi
    Hi again. I tried to install the APBS in other machine using the binary from Source Forge, and after fixing some problems with the Library path I was able to make it run. However it's only using 1 thread, any clue why is that?
    Naty Clementi
    @ncclementi
    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
    Arvind
    @Arvindiyer
    Hey I am getting CMake Error: File /src/.config/apbscfg.h.in does not exist.
    CMake Error at CMakeLists.txt:72 (configure_file):
    configure_file Problem configuring file this error while installing the apbs
    Juan
    @kozlac
    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.
    Juan
    @kozlac

    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$ make

    Please let me know if this helped. Thanks!!

    Arvind
    @Arvindiyer
    @kozlac your solution worked. Thanks 😊
    Stephan Bücker
    @Steviee22_gitlab

    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