## [apbs-users] Occupancy of a molecule on the grid

 [apbs-users] Occupancy of a molecule on the grid From: Davide Mercadante - 2013-01-17 02:12:45 Attachments: Message as HTML ```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 ```

 [apbs-users] Occupancy of a molecule on the grid From: Davide Mercadante - 2013-01-17 02:12:45 Attachments: Message as HTML ```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 ```
 Re: [apbs-users] Occupancy of a molecule on the grid From: Baker, Nathan - 2013-01-17 23:18:25 ```Hi Davide -- The "psize.py" script provided with APBS (tools/manip/psize.py or http://sourceforge.net/p/apbs/code/ci/9527462a39126fb6cd880924b3cc4880ec4b78a9/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 > Date: Wednesday, January 16, 2013 5:41 PM To: APBS-USERS mailing list >, APBS-USERS mailing list > 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 ```
 Re: [apbs-users] Occupancy of a molecule on the grid From: Davide Mercadante - 2013-01-19 21:36:00 ```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" wrote: >Hi Davide -- > >The "psize.py" script provided with APBS (tools/manip/psize.py or >http://sourceforge.net/p/apbs/code/ci/9527462a39126fb6cd880924b3cc4880ec4b >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 >> >Date: Wednesday, January 16, 2013 5:41 PM >To: APBS-USERS mailing list > >>, APBS-USERS mailing list >>> >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 > ```
 Re: [apbs-users] Occupancy of a molecule on the grid From: Baker, Nathan - 2013-01-19 21:31:39 ```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" 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" 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 >>> >>Date: Wednesday, January 16, 2013 5:41 PM >>To: APBS-USERS mailing list >>>> >>>, APBS-USERS mailing list >>>> >>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 >> > > ```
 Re: [apbs-users] Occupancy of a molecule on the grid From: Davide Mercadante - 2013-01-19 22:13:28 ```Yes, it happens exactly the same.. Thank you. D. On 19/01/2013, at 10:31 PM, "Baker, Nathan" wrote: > 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" 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" 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 >>> > >>> Date: Wednesday, January 16, 2013 5:41 PM >>> To: APBS-USERS mailing list >>> >>> >>>> , APBS-USERS mailing list >>>> > >>> 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 > ```