Wed Dec 28 11:02:00 PST 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 Wed Dec 28 2011 at 11:02:00 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6383704 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): -5.822000 35.46600 ymin,ymax (A): -3.677000 49.12100 zmin,zma (A): -24.52100 31.24600 x,y,z range (A): 41.28800 52.79800 55.76700 scale (grids/A): 0.6383704 object centre (A): 14.82200 22.72200 3.362500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8020 centred at (gu) : 90.75933 92.46372 90.23906 assigned negative charge : -288.4403 centred at (gu) : 90.91115 92.60497 90.17068 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5642 nv = 96 ne = 84 npr = 39363 no. pairs analyzed = 39363 no. exposed pairs = 2524 no. arc points = 17801 no. surface atoms = 855 nbur = 1111 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3146 m= 0 mr = 58 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1757 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5016985E-10 1.1209379E-08 midg,1,midg; midg,igrid,midg 9.7880184E-09 -1.1868039E-08 1,midg,midg; igrid,midg,midg 1.4740376E-08 -9.0547250E-09 gauss-seidel spectral radius is 0.9872355 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 11:02:01 rms-change max change #iterations 0.1283353 21.79238 at 10iterations 1.2463412E-02 2.073040 at 20iterations 1.2279381E-03 0.2101021 at 30iterations 1.1736980E-04 1.7159462E-02 at 40iterations 1.1632169E-05 1.9807816E-03 at 50iterations finished qdiffx linear iterations at : 11:02:05 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 1.1632169E-05 1.9807816E-03 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.870000 DelPhi exited at 11:02:08 4.878u 0.327s 0:07.95 65.2% 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 Wed Dec 28 2011 at 11:02:09 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.915111 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): -5.822000 35.46600 ymin,ymax (A): -3.677000 49.12100 zmin,zma (A): -24.52100 31.24600 x,y,z range (A): 41.28800 52.79800 55.76700 scale (grids/A): 1.915111 object centre (A): 14.82200 22.72200 3.362500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8020 centred at (gu) : 92.27800 97.39127 90.71753 assigned negative charge : -288.4403 centred at (gu) : 92.73372 97.81505 90.51228 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17801 grid for indexing accessible points = 1.400000 m= 23468 mr = 41354 m= 4177 mr = 18248 m= 252 mr = 3017 m= 1 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1297 time to turn everything in is 0.5700000 number of dielectric boundary points 25387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14453 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) : 0.6383704 object centre at (A) : 14.82200 22.72200 3.362500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3230936E-02 1.2749887E-02 midg,1,midg; midg,igrid,midg 3.0263014E-02 -9.8001156E-03 1,midg,midg; igrid,midg,midg 9.5336027E-03 -4.3465160E-03 gauss-seidel spectral radius is 0.9985772 estimated iterations to convergence 210 setup time was (sec) 0.9100000 now iterating at: 11:02:10 rms-change max change #iterations 3.647396 177.7727 at 10iterations 1.682388 66.09646 at 20iterations 0.7776128 29.88540 at 30iterations 0.3588442 13.41393 at 40iterations 0.1650877 6.408870 at 50iterations 7.5942338E-02 2.554184 at 60iterations 3.5006754E-02 1.255292 at 70iterations 1.6087502E-02 0.5470848 at 80iterations 7.4419552E-03 0.2777023 at 90iterations 3.4312673E-03 0.1146622 at 100iterations 1.5810890E-03 5.2906036E-02 at 110iterations 7.2620146E-04 2.6849747E-02 at 120iterations finished qdiffx linear iterations at : 11:02:21 total time elapsed so far: 11.92000 # loops : 120 mean,max change (kT/e) : 7.2620146E-04 2.6849747E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 11:02:22 12.100u 0.426s 0:13.62 91.9% 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 Wed Dec 28 2011 at 11:02:22 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.872667 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): -5.822000 35.46600 ymin,ymax (A): -3.677000 49.12100 zmin,zma (A): -24.52100 31.24600 x,y,z range (A): 41.28800 52.79800 55.76700 scale (grids/A): 2.872667 object centre (A): 14.82200 22.72200 3.362500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8020 centred at (gu) : 93.41700 101.0871 91.07623 assigned negative charge : -288.4403 centred at (gu) : 94.10059 101.7227 90.76844 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 138792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17801 grid for indexing accessible points = 1.400000 m= 73592 mr = 99664 m= 29485 mr = 61666 m= 7780 mr = 24964 m= 1153 mr = 6413 m= 70 mr = 853 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 4659 time to turn everything in is 1.420000 number of dielectric boundary points 57272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 14656 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) : 1.915111 object centre at (A) : 14.82200 22.72200 3.362500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.070633 -5.5058557E-03 midg,1,midg; midg,igrid,midg 0.2889666 -0.1173059 1,midg,midg; igrid,midg,midg 5.9932698E-02 -1.7105361E-02 gauss-seidel spectral radius is 0.9992310 estimated iterations to convergence 285 setup time was (sec) 1.810000 now iterating at: 11:02:24 rms-change max change #iterations 8.609117 423.5992 at 10iterations 4.940352 132.7601 at 20iterations 2.808224 73.22294 at 30iterations 1.602387 32.84131 at 40iterations 0.9100432 21.21647 at 50iterations 0.5169378 11.42970 at 60iterations 0.2934701 6.756477 at 70iterations 0.1664191 3.210995 at 80iterations 9.4354726E-02 1.917122 at 90iterations 5.3601705E-02 1.195528 at 100iterations 3.0321920E-02 0.6500406 at 110iterations 1.7277362E-02 0.3364563 at 120iterations 9.7644217E-03 0.1903639 at 130iterations 5.5428259E-03 0.1061592 at 140iterations 3.1406202E-03 5.8962345E-02 at 150iterations 1.7849704E-03 3.3560038E-02 at 160iterations 1.0132038E-03 1.9127846E-02 at 170iterations 5.7361781E-04 1.1184692E-02 at 180iterations finished qdiffx linear iterations at : 11:02:43 total time elapsed so far: 20.06000 # loops : 180 mean,max change (kT/e) : 5.7361781E-04 1.1184692E-02 energy calculations done at 20.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.25000 DelPhi exited at 11:02:44 20.247u 0.434s 0:22.27 92.8% 0+0k 0+0io 0pf+0w