Sun Oct 9 00:20:40 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 Sun Oct 9 2011 at 00:20:40 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: HIT 81 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 0.5746291 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): -15.94300 40.56900 ymin,ymax (A): 16.47800 76.41200 zmin,zma (A): 25.55700 87.51000 x,y,z range (A): 56.51200 59.93401 61.95300 scale (grids/A): 0.5746291 object centre (A): 12.31300 46.44500 56.53350 number of atom coordinates read : 3254 total number of charged atoms : 3113 net assigned charge : 12.97103 assigned positive charge : 482.0078 centred at (gu) : 89.79128 90.01519 90.61281 assigned negative charge : -469.0384 centred at (gu) : 89.64642 90.03925 90.80348 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7402 nv = 96 ne = 84 npr = 63633 no. pairs analyzed = 63633 no. exposed pairs = 4240 no. arc points = 30878 no. surface atoms = 1415 nbur = 1839 mkacc time = 0.1400000 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= 327 mr = 3809 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3146 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9347 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1984048E-09 -1.6446506E-09 midg,1,midg; midg,igrid,midg 2.8415137E-09 1.9243336E-09 1,midg,midg; igrid,midg,midg -5.0553389E-10 4.9026880E-09 gauss-seidel spectral radius is 0.9844083 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 00:20:41 rms-change max change #iterations 0.1007265 18.96236 at 10iterations 7.6460126E-03 1.313972 at 20iterations 6.0588232E-04 8.2624435E-02 at 30iterations 5.5710392E-05 8.4867477E-03 at 40iterations 7.0533602E-06 8.0490112E-04 at 50iterations finished qdiffx linear iterations at : 00:20:44 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 7.0533602E-06 8.0490112E-04 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 00:20:44 3.202u 0.182s 0:03.74 90.3% 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 Sun Oct 9 2011 at 00:20:44 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: HIT 81 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 1.723887 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): -15.94300 40.56900 ymin,ymax (A): 16.47800 76.41200 zmin,zma (A): 25.55700 87.51000 x,y,z range (A): 56.51200 59.93401 61.95300 scale (grids/A): 1.723887 object centre (A): 12.31300 46.44500 56.53350 number of atom coordinates read : 3254 total number of charged atoms : 3113 net assigned charge : 12.97103 assigned positive charge : 482.0078 centred at (gu) : 89.37269 90.04495 91.83760 assigned negative charge : -469.0384 centred at (gu) : 88.93916 90.11736 92.41023 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30878 grid for indexing accessible points = 1.400000 m= 26323 mr = 54655 m= 3229 mr = 18188 m= 119 mr = 1638 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 758 time to turn everything in is 0.5600000 number of dielectric boundary points 36293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 24151 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) : 0.5746291 object centre at (A) : 12.31300 46.44500 56.53350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9634002E-02 7.4845403E-03 midg,1,midg; midg,igrid,midg 3.7209436E-02 1.7601419E-02 1,midg,midg; igrid,midg,midg -9.1563286E-03 1.5613220E-02 gauss-seidel spectral radius is 0.9984252 estimated iterations to convergence 200 setup time was (sec) 0.8400000 now iterating at: 00:20:45 rms-change max change #iterations 3.897718 148.2249 at 10iterations 1.714936 61.10360 at 20iterations 0.7586589 25.03407 at 30iterations 0.3349149 11.00090 at 40iterations 0.1480306 4.895454 at 50iterations 6.5581232E-02 2.071060 at 60iterations 2.9061213E-02 0.8724136 at 70iterations 1.2865429E-02 0.4608650 at 80iterations 5.6757228E-03 0.1898403 at 90iterations 2.5123726E-03 9.7722828E-02 at 100iterations 1.1158517E-03 3.4986496E-02 at 110iterations 4.9357652E-04 1.4834225E-02 at 120iterations finished qdiffx linear iterations at : 00:20:52 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 4.9357652E-04 1.4834225E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 00:20:52 7.508u 0.221s 0:08.08 95.5% 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 Sun Oct 9 2011 at 00:20:52 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: HIT 81 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.585831 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): -15.94300 40.56900 ymin,ymax (A): 16.47800 76.41200 zmin,zma (A): 25.55700 87.51000 x,y,z range (A): 56.51200 59.93401 61.95300 scale (grids/A): 2.585831 object centre (A): 12.31300 46.44500 56.53350 number of atom coordinates read : 3254 total number of charged atoms : 3113 net assigned charge : 12.97103 assigned positive charge : 482.0078 centred at (gu) : 89.05867 90.06699 92.75604 assigned negative charge : -469.0384 centred at (gu) : 88.40882 90.17595 93.61526 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 188446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30878 grid for indexing accessible points = 1.400000 m= 88718 mr = 133842 m= 27604 mr = 70159 m= 5349 mr = 21014 m= 537 mr = 3583 m= 14 mr = 280 m= 0 mr = 2 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 2480 time to turn everything in is 1.380000 number of dielectric boundary points 81788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 24873 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) : 1.723887 object centre at (A) : 12.31300 46.44500 56.53350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7317347 9.7081721E-02 midg,1,midg; midg,igrid,midg 0.6126831 0.3482128 1,midg,midg; igrid,midg,midg -7.2416276E-02 0.2235015 gauss-seidel spectral radius is 0.9992265 estimated iterations to convergence 284 setup time was (sec) 1.670000 now iterating at: 00:20:54 rms-change max change #iterations 9.860423 291.4796 at 10iterations 5.745800 128.0718 at 20iterations 3.328744 74.03812 at 30iterations 1.915951 46.39742 at 40iterations 1.096883 24.28718 at 50iterations 0.6285999 13.56758 at 60iterations 0.3584207 7.529297 at 70iterations 0.2045196 4.606453 at 80iterations 0.1164542 2.228405 at 90iterations 6.6255540E-02 1.400711 at 100iterations 3.7677117E-02 0.7043101 at 110iterations 2.1343501E-02 0.3641624 at 120iterations 1.2132579E-02 0.2237377 at 130iterations 6.8889363E-03 0.1205122 at 140iterations 3.9080107E-03 6.8922043E-02 at 150iterations 2.2190819E-03 4.4643402E-02 at 160iterations 1.2589096E-03 2.4909973E-02 at 170iterations 7.1415707E-04 1.3169289E-02 at 180iterations finished qdiffx linear iterations at : 00:21:05 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 7.1415707E-04 1.3169289E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 00:21:05 12.245u 0.221s 0:12.73 97.8% 0+0k 0+0io 0pf+0w