Mon Oct 10 19:37:57 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+sph.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 = amb.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 Mon Oct 10 2011 at 19:37:57 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: CME 1 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6264628 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): -42.94100 10.51400 ymin,ymax (A): -15.99100 40.43300 zmin,zma (A): -46.05800 10.76900 x,y,z range (A): 53.45500 56.42400 56.82700 scale (grids/A): 0.6264628 object centre (A): -16.21350 12.22100 -17.64450 number of atom coordinates read : 2875 total number of charged atoms : 2731 net assigned charge : -3.034987 assigned positive charge : 431.5704 centred at (gu) : 91.10998 89.38861 89.60112 assigned negative charge : -434.6066 centred at (gu) : 91.12798 89.40803 89.61022 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7605 nv = 96 ne = 84 npr = 57670 no. pairs analyzed = 57670 no. exposed pairs = 3989 no. arc points = 28419 no. surface atoms = 1310 nbur = 1565 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 3795 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2746 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9159 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3335054E-09 -3.4706509E-09 midg,1,midg; midg,igrid,midg -1.3835340E-09 -4.1263792E-09 1,midg,midg; igrid,midg,midg -1.0900456E-09 -5.8195133E-09 gauss-seidel spectral radius is 0.9868401 estimated iterations to convergence 71 setup time was (sec) 0.6000000 now iterating at: 19:37:57 rms-change max change #iterations 0.1366744 22.10114 at 10iterations 1.2831331E-02 1.748432 at 20iterations 1.2242191E-03 0.1584053 at 30iterations 1.2000939E-04 1.4823914E-02 at 40iterations 1.3895107E-05 2.1400452E-03 at 50iterations finished qdiffx linear iterations at : 19:38:00 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.3895107E-05 2.1400452E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 19:38:01 3.667u 0.212s 0:04.19 92.3% 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 Mon Oct 10 2011 at 19:38:01 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: CME 1 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.879388 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): -42.94100 10.51400 ymin,ymax (A): -15.99100 40.43300 zmin,zma (A): -46.05800 10.76900 x,y,z range (A): 53.45500 56.42400 56.82700 scale (grids/A): 1.879388 object centre (A): -16.21350 12.22100 -17.64450 number of atom coordinates read : 2875 total number of charged atoms : 2731 net assigned charge : -3.034987 assigned positive charge : 431.5704 centred at (gu) : 93.32915 88.16497 88.80260 assigned negative charge : -434.6066 centred at (gu) : 93.38371 88.22376 88.83039 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28419 grid for indexing accessible points = 1.400000 m= 27536 mr = 54037 m= 4100 mr = 18967 m= 188 mr = 2208 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 38864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21451 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) : 0.6264628 object centre at (A) : -16.21350 12.22100 -17.64450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9116910E-02 -8.9778714E-03 midg,1,midg; midg,igrid,midg -2.8928099E-03 6.0212507E-04 1,midg,midg; igrid,midg,midg -3.8854573E-03 7.9040704E-03 gauss-seidel spectral radius is 0.9986466 estimated iterations to convergence 215 setup time was (sec) 0.9500000 now iterating at: 19:38:02 rms-change max change #iterations 4.431389 220.9668 at 10iterations 2.068825 72.87202 at 20iterations 0.9659970 30.59473 at 30iterations 0.4535325 13.92554 at 40iterations 0.2129105 7.231218 at 50iterations 9.9773169E-02 3.093387 at 60iterations 4.6819817E-02 1.456133 at 70iterations 2.1955309E-02 0.7644653 at 80iterations 1.0264583E-02 0.3191791 at 90iterations 4.8377104E-03 0.1417570 at 100iterations 2.2708641E-03 7.1897030E-02 at 110iterations 1.0694579E-03 3.4397125E-02 at 120iterations finished qdiffx linear iterations at : 19:38:09 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 1.0694579E-03 3.4397125E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 19:38:10 8.123u 0.196s 0:08.83 94.1% 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 Mon Oct 10 2011 at 19:38:10 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: CME 1 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.819082 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): -42.94100 10.51400 ymin,ymax (A): -15.99100 40.43300 zmin,zma (A): -46.05800 10.76900 x,y,z range (A): 53.45500 56.42400 56.82700 scale (grids/A): 2.819082 object centre (A): -16.21350 12.22100 -17.64450 number of atom coordinates read : 2875 total number of charged atoms : 2731 net assigned charge : -3.034987 assigned positive charge : 431.5704 centred at (gu) : 94.99345 87.24741 88.20380 assigned negative charge : -434.6066 centred at (gu) : 95.07557 87.33573 88.24567 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 190494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28419 grid for indexing accessible points = 1.400000 m= 89557 mr = 132260 m= 31082 mr = 70301 m= 6964 mr = 23563 m= 818 mr = 4751 m= 31 mr = 466 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 87602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 21845 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) : 1.879388 object centre at (A) : -16.21350 12.22100 -17.64450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3843732 -7.9825349E-02 midg,1,midg; midg,igrid,midg -1.2611325E-03 7.0527069E-02 1,midg,midg; igrid,midg,midg -6.1849605E-02 0.2340870 gauss-seidel spectral radius is 0.9992814 estimated iterations to convergence 294 setup time was (sec) 1.930000 now iterating at: 19:38:12 rms-change max change #iterations 10.57134 335.1169 at 10iterations 6.289350 143.3707 at 20iterations 3.715786 81.05099 at 30iterations 2.180138 43.87613 at 40iterations 1.277562 27.30062 at 50iterations 0.7463440 12.84799 at 60iterations 0.4354400 8.997885 at 70iterations 0.2532173 4.928590 at 80iterations 0.1470220 2.734073 at 90iterations 8.5428931E-02 1.517227 at 100iterations 4.9587153E-02 0.8891335 at 110iterations 2.8796004E-02 0.5259141 at 120iterations 1.6698821E-02 0.2976799 at 130iterations 9.6766613E-03 0.1659412 at 140iterations 5.6119887E-03 9.7228050E-02 at 150iterations 3.2529531E-03 5.7395093E-02 at 160iterations 1.8922883E-03 3.2272339E-02 at 170iterations 1.0992467E-03 1.9471169E-02 at 180iterations finished qdiffx linear iterations at : 19:38:23 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 1.0992467E-03 1.9471169E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 19:38:24 13.451u 0.205s 0:13.96 97.7% 0+0k 0+0io 0pf+0w