{"action":"created","issue":{"url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/174","labels_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/174/labels{/name}","comments_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/174/comments","events_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/174/events","html_url":"https://github.com/Electrostatics/apbs-pdb2pqr/issues/174","id":39768155,"number":174,"title":"Investigate focus calculation","user":{"login":"keith923","id":6402836,"avatar_url":"https://avatars.githubusercontent.com/u/6402836?v=3","gravatar_id":"","url":"https://api.github.com/users/keith923","html_url":"https://github.com/keith923","followers_url":"https://api.github.com/users/keith923/followers","following_url":"https://api.github.com/users/keith923/following{/other_user}","gists_url":"https://api.github.com/users/keith923/gists{/gist_id}","starred_url":"https://api.github.com/users/keith923/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/keith923/subscriptions","organizations_url":"https://api.github.com/users/keith923/orgs","repos_url":"https://api.github.com/users/keith923/repos","events_url":"https://api.github.com/users/keith923/events{/privacy}","received_events_url":"https://api.github.com/users/keith923/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/labels/apbs","name":"apbs","color":"fbca04"},{"url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/labels/investigate","name":"investigate","color":"bfe5bf"}],"state":"open","locked":false,"assignee":{"login":"kozlac","id":13038084,"avatar_url":"https://avatars.githubusercontent.com/u/13038084?v=3","gravatar_id":"","url":"https://api.github.com/users/kozlac","html_url":"https://github.com/kozlac","followers_url":"https://api.github.com/users/kozlac/followers","following_url":"https://api.github.com/users/kozlac/following{/other_user}","gists_url":"https://api.github.com/users/kozlac/gists{/gist_id}","starred_url":"https://api.github.com/users/kozlac/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kozlac/subscriptions","organizations_url":"https://api.github.com/users/kozlac/orgs","repos_url":"https://api.github.com/users/kozlac/repos","events_url":"https://api.github.com/users/kozlac/events{/privacy}","received_events_url":"https://api.github.com/users/kozlac/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/milestones/24","html_url":"https://github.com/Electrostatics/apbs-pdb2pqr/milestones/APBS%201.4.2%20release","labels_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/milestones/24/labels","id":1207413,"number":24,"title":"APBS 1.4.2 release","description":"","creator":{"login":"lizutah","id":1486218,"avatar_url":"https://avatars.githubusercontent.com/u/1486218?v=3","gravatar_id":"","url":"https://api.github.com/users/lizutah","html_url":"https://github.com/lizutah","followers_url":"https://api.github.com/users/lizutah/followers","following_url":"https://api.github.com/users/lizutah/following{/other_user}","gists_url":"https://api.github.com/users/lizutah/gists{/gist_id}","starred_url":"https://api.github.com/users/lizutah/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lizutah/subscriptions","organizations_url":"https://api.github.com/users/lizutah/orgs","repos_url":"https://api.github.com/users/lizutah/repos","events_url":"https://api.github.com/users/lizutah/events{/privacy}","received_events_url":"https://api.github.com/users/lizutah/received_events","type":"User","site_admin":false},"open_issues":22,"closed_issues":2,"state":"open","created_at":"2015-07-14T17:06:34Z","updated_at":"2015-08-31T21:44:03Z","due_on":"2015-10-01T07:00:00Z","closed_at":null},"comments":1,"created_at":"2014-08-07T21:04:14Z","updated_at":"2015-08-31T21:44:52Z","closed_at":null,"body":"From a user:\r\n> -----Original Message-----\r\n> From: Marcelo Marucho [mailto:marcelo.marucho@utsa.edu]\r\n> Sent: Wednesday, August 06, 2014 12:10\r\n> To: Baker, Nathan\r\n> Subject: update focus calculation\r\n> \r\n> Dear Nathan\r\n> \r\n> I am sending you the comparison between APBS and MAPBS using focusing.\r\n> \r\n> As far as all atoms in the system are inside the box (for both coarse and fine grids) we are obtaining a good comparison between APBS and MAPBS.\r\n> \r\n> In the case in which some atoms of the system are outside the box (and even without using focusing), apbs is getting unusual large values for the solution of PB equation for the two systems we analyzed here. (I think this issue is generated by the multigrid approach implemented  in apbs).\r\n> \r\n> As far as testing focusing, I think the comparison between MAPBS and apbs looks OK.\r\n> \r\n> I also realized that we were using the old version of \"sdh\" calculation where only a monopole was used to calculate the potential at the boundary condition. Now I included in MAPBS the multipole expansion for sdh including monopole, dipole and quadrupole contributions and it works perfect. We observed very small differences using both definitions for sdh in the examples we were testing and comparing apbs and MAPBS.\r\n> \r\n> Please let me know your feedback.\r\n> \r\n> Many thanks\r\n> \r\n> Marcelo"},"comment":{"url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/comments/136510053","html_url":"https://github.com/Electrostatics/apbs-pdb2pqr/issues/174#issuecomment-136510053","issue_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/174","id":136510053,"user":{"login":"keith923","id":6402836,"avatar_url":"https://avatars.githubusercontent.com/u/6402836?v=3","gravatar_id":"","url":"https://api.github.com/users/keith923","html_url":"https://github.com/keith923","followers_url":"https://api.github.com/users/keith923/followers","following_url":"https://api.github.com/users/keith923/following{/other_user}","gists_url":"https://api.github.com/users/keith923/gists{/gist_id}","starred_url":"https://api.github.com/users/keith923/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/keith923/subscriptions","organizations_url":"https://api.github.com/users/keith923/orgs","repos_url":"https://api.github.com/users/keith923/repos","events_url":"https://api.github.com/users/keith923/events{/privacy}","received_events_url":"https://api.github.com/users/keith923/received_events","type":"User","site_admin":false},"created_at":"2015-08-31T21:44:52Z","updated_at":"2015-08-31T21:44:52Z","body":"Attachment from email follows.\r\n```\r\nGrid: 129 129 129\r\nCoarse grid lenght: 96 96 96\r\nFine grid lenght: 57 57 57 \r\nFine Grid spacing: 0.445\r\nchgm: spl0\r\nbc: mdh\r\nionic strength: 0 M\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\nGrid: 129 129 129\r\nCoarse grid lenght: 96 96 96\r\nFine grid lenght: 57 57 57 \r\nFine Grid spacing: 0.445\r\nsrfm: mol\r\nchgm: spl0\r\nbc: mdh\r\nionic strength: 0.010 M\r\n\r\n\r\n\r\n\r\n\r\n\r\n########################################################################## \r\n### HCA/ACETAZOLAMIDE BINDING \r\n### $Id$ \r\n### \r\n###  Please see APBS documentation (http://apbs.sourceforge.net/doc/) for \r\n### syntax help. \r\n########################################################################## \r\n\r\nread \r\n    mol pqr acet.pqr                    # Read molecule 1 \r\n    mol pqr hca.pqr                    # Read molecule 1 \r\n    mol pqr complex.pqr                   # Read molecule 1 \r\nend \r\n\r\n# ACETAZOLAMIDE POTENTIAL \r\nelec name acet \r\n    mg-auto \r\n    dime 129 129 129 \r\n    cglen 96.0 96.0 96.0 \r\n    fglen 57 57 57 \r\n    fgcent mol 2 \r\n    cgcent mol 2 \r\n    mol 1 \r\n    lpbe \r\n    bcfl mdh \r\n    #ion charge 1 conc 0.000 radius 2.0                    \r\n    #ion charge -1 conc 0.000 radius 2.0                \r\n    pdie 2.0 \r\n    sdie 78.54 \r\n    chgm spl0 \r\n    srfm mol \r\n    srad 0.0 \r\n    swin 0.3 \r\n    sdens 10.0 \r\n    temp 298.15 \r\n    calcenergy total \r\n    calcforce no \r\n  \r\nend \r\n\r\n# HCA POTENTIAL \r\nelec name hca \r\n    mg-auto \r\n    dime 129 129 129 \r\n    cglen 96.0 96.0 96.0 \r\n    fglen 57 57 57 \r\n    fgcent mol 2 \r\n    cgcent mol 2 \r\n    mol 2 \r\n    lpbe \r\n    bcfl mdh \r\n    #ion charge 1 conc 0.000 radius 2.0               \r\n    #ion charge -1 conc 0.000 radius 2.0               \r\n    pdie 2.0 \r\n    sdie 78.54 \r\n    chgm spl0 \r\n    srfm mol \r\n    srad 0.0 \r\n    swin 0.3 \r\n    sdens 10.0 \r\n    temp 298.15 \r\n    calcenergy total \r\n    calcforce no \r\n end \r\n\r\n# COMPLEX POTENTIAL \r\nelec name complex \r\n    mg-auto \r\n    dime 129 129 129 \r\n    cglen 96.0 96.0 96.0 \r\n    fglen 57 57 57 \r\n    fgcent mol 2 \r\n    cgcent mol 2 \r\n    mol 3 \r\n    lpbe \r\n    bcfl mdh \r\n    #ion charge 1 conc 0.000 radius 2.0               \r\n    #ion charge -1 conc 0.000 radius 2.0      \r\n    pdie 2.0 \r\n    sdie 78.54 \r\n    chgm spl0 \r\n    srfm mol \r\n    srad 0.0 \r\n    swin 0.3 \r\n    sdens 10.0 \r\n    temp 298.15 \r\n    calcenergy total \r\n    calcforce no \r\n end \r\n\r\n# CALCULATE BINDING ENERGY \r\nprint elecEnergy acet end \r\nprint elecEnergy hca end \r\nprint elecEnergy complex end \r\nprint elecEnergy complex - acet - hca end \r\nquit\r\n\r\n\r\n########################################################################## \r\n### 1D7H/DMSO BINDING ENERGY \r\n### $Id$ \r\n### \r\n### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for \r\n### syntax help. \r\n########################################################################## \r\n\r\nread \r\n  mol pqr 1d7h-dmso-complex.pqr \r\n  mol pqr 1d7h-min.pqr \r\n  mol pqr dmso-min.pqr \r\nend \r\n\r\n# 1D7H -- SOLVATED STATE (FOCUSING) \r\nelec name 1d7h \r\n    mg-auto \r\n    dime 129 129 129 \r\n    cglen 96.0 96.0 96.0 \r\n    fglen 57 57 57 \r\n    fgcent mol 2 \r\n    cgcent mol 2 \r\n    mol 2 \r\n    lpbe \r\n    bcfl mdh \r\n    ion charge 1 conc 0.010 radius 2.0 \r\n    ion charge -1 conc 0.010 radius 2.0 \r\n    pdie  2.0 \r\n    sdie 78.0 \r\n    srfm mol \r\n    chgm spl0 \r\n    srad 0.0 \r\n    swin 0.3 \r\n    sdens 10.0 \r\n    temp 300 \r\n    calcenergy total \r\n    calcforce no \r\n  end \r\nelec name dmso \r\n    mg-auto \r\n    dime 129 129 129 \r\n    cglen 96.0 96.0 96.0 \r\n    fglen 57 57 57 \r\n    fgcent mol 2 \r\n    cgcent mol 2 \r\n    mol 3 \r\n    lpbe \r\n    bcfl mdh \r\n    ion charge 1 conc 0.010 radius 2.0 \r\n    ion charge -1 conc 0.010 radius 2.0 \r\n    pdie  2.0 \r\n    sdie 78.0 \r\n    srfm mol \r\n    chgm spl0 \r\n    srad 0.0 \r\n    swin 0.3 \r\n    sdens 10.0 \r\n    temp 300 \r\n    calcenergy total \r\n    calcforce no \r\n  end \r\nelec name complex \r\n    mg-auto \r\n    dime 129 129 129 \r\n    cglen 96.0 96.0 96.0 \r\n    fglen 57 57 57 \r\n    fgcent mol 2 \r\n    cgcent mol 2 \r\n    mol 1 \r\n    lpbe \r\n    bcfl mdh \r\n    ion charge 1 conc 0.010 radius 2.0 \r\n    ion charge -1 conc 0.010 radius 2.0 \r\n    pdie  2.0 \r\n    sdie 78.0 \r\n    srfm mol \r\n    chgm spl0 \r\n    srad 0.0 \r\n    swin 0.3 \r\n    sdens 10.0 \r\n    temp 300 \r\n    calcenergy total \r\n    calcforce no \r\n  end \r\n\r\nquit\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\nMAPBS acetazolamide\r\n//acet_focus.inm\r\n129 129 129 \r\n57.000000 57.000000 57.000000 \r\n0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000 \r\nfocusname.inm \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nacet.pqr \r\nhca.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\n// focusname.inm\r\n129 129 129 \r\n96.000000 96.000000 96.000000 \r\n0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000 \r\nmdh \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nacet.pqr \r\nhca.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\nMAPBS hca\r\n//hca_bigbox.inm\r\n129 129 129 \r\n57.000000 57.000000 57.000000 \r\n0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000 \r\nfocusname.inm \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nhca.pqr \r\nhca.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\n\r\n//focusname.inm\r\n129 129 129 \r\n96.000000 96.000000 96.000000 \r\n0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000 \r\nmdh \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nhca.pqr \r\nhca.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\nMAPBS hca-acetazolamide\r\n//complex_bigbox2.inm\r\n129 129 129 \r\n57.000000 57.000000 57.000000 \r\n0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000 \r\nfocusname.inm \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\ncomplex.pqr \r\nhca.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\n\r\n//focusname.inm\r\n129 129 129 \r\n96.000000 96.000000 96.000000 \r\n0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000 \r\nmdh \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\ncomplex.pqr \r\nhca.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\nMAPBS 1d7h-dmso-complex\r\n\r\n//1d7h-dmso-complex_bigbox\r\n129 129 129 \r\n57.000000 57.000000 57.000000 \r\n0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000 \r\nfocusname.inm \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\n1d7h-dmso-complex.pqr \r\n1d7h-min.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\n\r\n// focusname.inm\r\n129 129 129 \r\n96.000000 96.000000 96.000000 \r\n0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000 \r\nmdh \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\n1d7h-dmso-complex.pqr \r\n1d7h-min.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\nMAPBS 1d7h\r\n//1d7h.inm\r\n129 129 129 \r\n57.000000 57.000000 57.000000 \r\n0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000 \r\nfocusname.inm \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\n1d7h-min.pqr \r\n1d7h-min.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\n\r\n//focusname.inm\r\n129 129 129 \r\n96.000000 96.000000 96.000000 \r\n0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000 \r\nmdh \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\n1d7h-min.pqr \r\n1d7h-min.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\nMAPBS dmso //dmso.inm\r\n129 129 129 \r\n57.000000 57.000000 57.000000 \r\n0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000 \r\nfocusname.inm \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\ndmso-min.pqr \r\n1d7h-min.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\n\r\n//focusname.inm\r\n129 129 129 \r\n96.000000 96.000000 96.000000 \r\n0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000 \r\nmdh \r\n6 biconjgrad \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\nnouploadedfiles \r\ndmso-min.pqr \r\n1d7h-min.pqr \r\nMOL \r\nSPL0 \r\ncalceneryes \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/ \r\n/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP \r\n1.000000 1.000000 1.000000 1.000000 1.000000\r\n```"}}