Re: [apbs-users] Occupancy of a molecule on the grid
Biomolecular electrostatics software
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From: Baker, N. <Nat...@pn...> - 2013-01-19 21:31:39
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Hello -- Have you tried downloading the Mac executable we provide? Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Phone: +1-509-375-3997 http://nabaker.me On 1/19/13 1:27 PM, "Davide Mercadante" <dm...@au...> wrote: >Dear Prof. Nathan Baker, > >Many thanks for your prompt reply. I will have a try at the script. >However, before having the possibility to try it, I tried to compile and >install apbs from source code on a MacBook Pro (early 2011) using cmake. >Compilation and installation were successful but when I try to launch the >freshly created executable I get the following error: > >dyld: Library not loaded: libmaloc.dylib > Referenced from: /Users/DMac/progs/apbs/bin/./apbs > Reason: image not found >Trace/BPT trap: 5 > >It looks like the executable is not able to load the library >"libmaloc.dylib" that is placed into the lib folder. >Running the command: > >otool -L /Users/DMac/progs/apbs/bin/apbs > >Gives the following: > >/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version >169.3.0) > libmaloc.dylib (compatibility version 0.0.0, current version 0.0.0) > /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version >1.2.5) > /Users/DMac/progs/apbs/lib/libapbs_generic.dylib (compatibility version >0.0.0, current version 0.0.0) > /Users/DMac/progs/apbs/lib/libapbs_pmgc.dylib (compatibility version >0.0.0, current version 0.0.0) > /Users/DMac/progs/apbs/lib/libapbs_mg.dylib (compatibility version 0.0.0, >current version 0.0.0) > >And shows that the libmaloc.dylib is the only one that doesn't have a >path. >Can you please help me to understand where the problem is and how I can >solve it? Please note that is happens exactly in the same way when I >download and try to launch the pre-compiled executable for MacOS. > >Thank you in advance for your kind reply. > >Cheers, >Davide > > > >On 17/01/13 3:18 PM, "Baker, Nathan" <Nat...@pn...> wrote: > >>Hi Davide -- >> >>The "psize.py" script provided with APBS (tools/manip/psize.py or >>http://sourceforge.net/p/apbs/code/ci/9527462a39126fb6cd880924b3cc4880ec4 >>b >>78a9/tree/tools/manip/psize.py) will provide some of this type of >>information. Have you tried that? >> >>Thanks, >> >>__________________________________________________ >>Nathan Baker >>Pacific Northwest National Laboratory >>Phone: +1-509-375-3997 >>http://nabaker.me >> >> >>From: Davide Mercadante >><dm...@au...<mailto:dm...@au...>> >>Date: Wednesday, January 16, 2013 5:41 PM >>To: APBS-USERS mailing list >><apb...@li...<mailto:apb...@li... >>> >>>, APBS-USERS mailing list >>><apb...@go...<mailto:apb...@go...>> >>Subject: [apbs-users] Occupancy of a molecule on the grid >> >>Dear APBS users, >> >>i have been performing electrostatic calculations on a macromolecular >>complex using APBS with the aim to have an electrostatic binding energy >>profile along a reaction trajectory (MD frames)... >> >>In order to do this and minimize accuracies I have chosen a focusing >>approach with grid dimensions of 161 A^3 (cubic grid) and glen variable >>across three calculations (an initial one (bcfl = zero) and two >>subsequent focusing calculations (bcfl = focus)) in which the glen was >>200, 100 and 75^3 respectively. >> >>I was wondering how I could calculate, how much of the complex occupies >>the grid in the three different glen conditions. Is there an empirical >>relation that allows me to calculate how much (percentage will do) of the >>complex is actually occupying the grid? >> >>I would expect that decreasing glen such percentage would increase. >> >>Can you please advice me on this? >> >>Thank you very much in advance for any response. >> >>Davide >> > > |