Sat Oct 15 14:25:08 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 14:25:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5890042 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -30.98500 29.45600 ymin,ymax (A): -24.74900 22.01100 zmin,zma (A): -7.509000 39.53900 x,y,z range (A): 60.44100 46.76000 47.04800 scale (grids/A): 0.5890042 object centre (A): -0.7644997 -1.369000 16.01500 number of atom coordinates read : 2819 total number of charged atoms : 2679 net assigned charge : -2.485970 assigned positive charge : 424.1353 centred at (gu) : 90.09461 89.71467 89.71655 assigned negative charge : -426.6223 centred at (gu) : 90.03986 89.88286 89.66010 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6524 nv = 96 ne = 84 npr = 56570 no. pairs analyzed = 56570 no. exposed pairs = 3708 no. arc points = 26193 no. surface atoms = 1257 nbur = 1562 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 288 mr = 3338 m= 0 mr = 8 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2688 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8221 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5192424E-09 7.8773182E-10 midg,1,midg; midg,igrid,midg 4.2078234E-09 -5.2523927E-09 1,midg,midg; igrid,midg,midg -2.2601658E-09 8.1569124E-10 gauss-seidel spectral radius is 0.9851118 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 14:25:09 rms-change max change #iterations 0.1026812 16.93502 at 10iterations 8.2585169E-03 1.364555 at 20iterations 6.7227770E-04 9.6332550E-02 at 30iterations 5.7436599E-05 8.3646774E-03 at 40iterations 5.5283926E-06 9.5176697E-04 at 50iterations finished qdiffx linear iterations at : 14:25:12 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 5.5283926E-06 9.5176697E-04 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 14:25:12 3.552u 0.199s 0:04.15 90.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 14:25:12 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.767012 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -30.98500 29.45600 ymin,ymax (A): -24.74900 22.01100 zmin,zma (A): -7.509000 39.53900 x,y,z range (A): 60.44100 46.76000 47.04800 scale (grids/A): 1.767012 object centre (A): -0.7644997 -1.369000 16.01500 number of atom coordinates read : 2819 total number of charged atoms : 2679 net assigned charge : -2.485970 assigned positive charge : 424.1353 centred at (gu) : 90.28307 89.14314 89.14901 assigned negative charge : -426.6223 centred at (gu) : 90.11926 89.64844 88.97987 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26193 grid for indexing accessible points = 1.400000 m= 22441 mr = 47540 m= 2401 mr = 15298 m= 83 mr = 1133 m= 0 mr = 5 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.3500000 number of dielectric boundary points 31889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20868 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5890042 object centre at (A) : -0.7644997 -1.369000 16.01500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4534213E-03 -1.1967480E-02 midg,1,midg; midg,igrid,midg 1.5902137E-02 -2.1810979E-02 1,midg,midg; igrid,midg,midg -2.3770810E-03 6.7678961E-04 gauss-seidel spectral radius is 0.9984519 estimated iterations to convergence 202 setup time was (sec) 0.5900000 now iterating at: 14:25:13 rms-change max change #iterations 3.837676 164.2516 at 10iterations 1.707836 66.47485 at 20iterations 0.7569805 25.62262 at 30iterations 0.3370191 11.49728 at 40iterations 0.1498270 5.028411 at 50iterations 6.6717073E-02 2.400219 at 60iterations 2.9718094E-02 1.055382 at 70iterations 1.3231119E-02 0.4320374 at 80iterations 5.8948793E-03 0.1859970 at 90iterations 2.6265197E-03 9.0418816E-02 at 100iterations 1.1711740E-03 3.9764404E-02 at 110iterations 5.2085071E-04 1.9056320E-02 at 120iterations finished qdiffx linear iterations at : 14:25:20 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 5.2085071E-04 1.9056320E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 14:25:21 8.058u 0.211s 0:08.54 96.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 14:25:21 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.650519 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -30.98500 29.45600 ymin,ymax (A): -24.74900 22.01100 zmin,zma (A): -7.509000 39.53900 x,y,z range (A): 60.44100 46.76000 47.04800 scale (grids/A): 2.650519 object centre (A): -0.7644997 -1.369000 16.01500 number of atom coordinates read : 2819 total number of charged atoms : 2679 net assigned charge : -2.485970 assigned positive charge : 424.1353 centred at (gu) : 90.42439 88.71455 88.72334 assigned negative charge : -426.6223 centred at (gu) : 90.17882 89.47258 88.46982 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 164517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26193 grid for indexing accessible points = 1.400000 m= 76139 mr = 116163 m= 22975 mr = 59781 m= 3744 mr = 17268 m= 291 mr = 2317 m= 2 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 270 time to turn everything in is 0.8700000 number of dielectric boundary points 72022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 21416 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.767012 object centre at (A) : -0.7644997 -1.369000 16.01500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5564357E-02 -0.2354696 midg,1,midg; midg,igrid,midg 0.2276924 -0.2318801 1,midg,midg; igrid,midg,midg 5.3267643E-02 9.1981225E-02 gauss-seidel spectral radius is 0.9992250 estimated iterations to convergence 284 setup time was (sec) 1.120000 now iterating at: 14:25:22 rms-change max change #iterations 9.565390 318.4060 at 10iterations 5.564301 142.2162 at 20iterations 3.199422 79.29769 at 30iterations 1.833814 40.22112 at 40iterations 1.050488 23.49463 at 50iterations 0.5987711 12.22107 at 60iterations 0.3412804 6.875733 at 70iterations 0.1939584 4.337873 at 80iterations 0.1103826 2.161121 at 90iterations 6.2697098E-02 1.197422 at 100iterations 3.5586730E-02 0.6737499 at 110iterations 2.0163089E-02 0.3866882 at 120iterations 1.1444258E-02 0.2313619 at 130iterations 6.4866459E-03 0.1220970 at 140iterations 3.6748676E-03 7.0034027E-02 at 150iterations 2.0833374E-03 3.8489819E-02 at 160iterations 1.1829456E-03 2.5986195E-02 at 170iterations 6.6963793E-04 1.3354778E-02 at 180iterations finished qdiffx linear iterations at : 14:25:34 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 6.6963793E-04 1.3354778E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 14:25:34 12.986u 0.235s 0:13.50 97.8% 0+0k 0+0io 0pf+0w