Sun Oct 9 14:11:16 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 14:11:16 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 184 has a net charge of -0.4750 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: 0.5747405 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): 0.1520001 51.51000 ymin,ymax (A): -12.38100 38.67400 zmin,zma (A): -15.10500 46.83600 x,y,z range (A): 51.35800 51.05500 61.94100 scale (grids/A): 0.5747405 object centre (A): 25.83100 13.14650 15.86550 number of atom coordinates read : 2671 total number of charged atoms : 2530 net assigned charge : 9.539018 assigned positive charge : 408.7827 centred at (gu) : 89.66916 91.64394 88.39818 assigned negative charge : -399.2446 centred at (gu) : 89.60780 91.49275 88.47390 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5826 nv = 96 ne = 84 npr = 52616 no. pairs analyzed = 52616 no. exposed pairs = 3470 no. arc points = 24582 no. surface atoms = 1164 nbur = 1507 mkacc time = 9.0000004E-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 = 1.512000 m= 284 mr = 2984 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2572 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7463 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2271942E-09 2.9538003E-10 midg,1,midg; midg,igrid,midg -5.7145266E-10 6.0743708E-09 1,midg,midg; igrid,midg,midg 6.8667888E-10 2.4680602E-09 gauss-seidel spectral radius is 0.9843538 estimated iterations to convergence 66 setup time was (sec) 0.3700000 now iterating at: 14:11:17 rms-change max change #iterations 9.0745635E-02 16.32602 at 10iterations 6.8141511E-03 1.235112 at 20iterations 5.3378992E-04 9.9334717E-02 at 30iterations 4.5226625E-05 9.1166496E-03 at 40iterations 5.6842628E-06 8.9645386E-04 at 50iterations finished qdiffx linear iterations at : 14:11:19 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 5.6842628E-06 8.9645386E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:11:20 3.327u 0.182s 0:03.78 92.5% 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 14:11:20 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 184 has a net charge of -0.4750 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: 1.724221 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): 0.1520001 51.51000 ymin,ymax (A): -12.38100 38.67400 zmin,zma (A): -15.10500 46.83600 x,y,z range (A): 51.35800 51.05500 61.94100 scale (grids/A): 1.724221 object centre (A): 25.83100 13.14650 15.86550 number of atom coordinates read : 2671 total number of charged atoms : 2530 net assigned charge : 9.539018 assigned positive charge : 408.7827 centred at (gu) : 89.00704 94.93096 85.19412 assigned negative charge : -399.2446 centred at (gu) : 88.82334 94.47821 85.42142 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24582 grid for indexing accessible points = 1.400000 m= 20430 mr = 42568 m= 2261 mr = 13894 m= 89 mr = 1046 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 28852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 19584 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) : 0.5747405 object centre at (A) : 25.83100 13.14650 15.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5147480E-02 1.6432904E-02 midg,1,midg; midg,igrid,midg 3.0211795E-03 2.0026917E-02 1,midg,midg; igrid,midg,midg -1.1143220E-02 8.3715627E-03 gauss-seidel spectral radius is 0.9983512 estimated iterations to convergence 195 setup time was (sec) 0.5200000 now iterating at: 14:11:21 rms-change max change #iterations 3.520578 161.3422 at 10iterations 1.521385 59.24791 at 20iterations 0.6637463 25.55010 at 30iterations 0.2873106 10.21352 at 40iterations 0.1250561 4.687735 at 50iterations 5.4368071E-02 1.855518 at 60iterations 2.3529006E-02 0.9065433 at 70iterations 1.0253213E-02 0.4677124 at 80iterations 4.4528148E-03 0.1628246 at 90iterations 1.9391082E-03 7.3899269E-02 at 100iterations 8.4385899E-04 3.2463074E-02 at 110iterations 3.6597936E-04 1.2178421E-02 at 120iterations finished qdiffx linear iterations at : 14:11:27 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 3.6597936E-04 1.2178421E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 14:11:28 7.577u 0.195s 0:08.16 95.0% 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 14:11:28 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 184 has a net charge of -0.4750 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: 2.586332 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): 0.1520001 51.51000 ymin,ymax (A): -12.38100 38.67400 zmin,zma (A): -15.10500 46.83600 x,y,z range (A): 51.35800 51.05500 61.94100 scale (grids/A): 2.586332 object centre (A): 25.83100 13.14650 15.86550 number of atom coordinates read : 2671 total number of charged atoms : 2530 net assigned charge : 9.539018 assigned positive charge : 408.7827 centred at (gu) : 88.51035 97.39637 82.79101 assigned negative charge : -399.2446 centred at (gu) : 88.23490 96.71720 83.13210 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 147493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24582 grid for indexing accessible points = 1.400000 m= 68957 mr = 103833 m= 20793 mr = 54148 m= 3521 mr = 15570 m= 304 mr = 2184 m= 10 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 65204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20225 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) : 1.724221 object centre at (A) : 25.83100 13.14650 15.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.059206 0.2579523 midg,1,midg; midg,igrid,midg 4.7045052E-02 0.1632474 1,midg,midg; igrid,midg,midg -0.1403481 0.1180175 gauss-seidel spectral radius is 0.9991816 estimated iterations to convergence 276 setup time was (sec) 1.010000 now iterating at: 14:11:29 rms-change max change #iterations 8.936648 377.1111 at 10iterations 5.169326 177.6984 at 20iterations 2.951908 79.45334 at 30iterations 1.678980 36.39666 at 40iterations 0.9504600 21.10925 at 50iterations 0.5363591 11.91466 at 60iterations 0.3019897 6.557716 at 70iterations 0.1700001 3.810959 at 80iterations 9.5377997E-02 2.115618 at 90iterations 5.3460658E-02 1.168913 at 100iterations 2.9980991E-02 0.6795502 at 110iterations 1.6790457E-02 0.3465080 at 120iterations 9.4069494E-03 0.1889362 at 130iterations 5.2587129E-03 0.1117783 at 140iterations 2.9330866E-03 5.9102654E-02 at 150iterations 1.6421303E-03 3.3477783E-02 at 160iterations 9.1769919E-04 1.7721653E-02 at 170iterations 5.1355525E-04 1.0910034E-02 at 180iterations finished qdiffx linear iterations at : 14:11:40 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 5.1355525E-04 1.0910034E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 14:11:41 12.099u 0.197s 0:12.56 97.7% 0+0k 0+0io 0pf+0w