Sat Oct 15 13:25:08 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+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 Sat Oct 15 2011 at 13:25:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5576004 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 0.5576004 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1943 total number of charged atoms : 1813 net assigned charge : 5.000010 assigned positive charge : 284.3641 centred at (gu) : 89.73518 90.05009 89.20637 assigned negative charge : -279.3644 centred at (gu) : 89.65081 90.20256 89.17575 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4122 nv = 96 ne = 84 npr = 38283 no. pairs analyzed = 38283 no. exposed pairs = 2484 no. arc points = 17910 no. surface atoms = 848 nbur = 1095 mkacc time = 7.0000008E-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 = 1.540000 m= 178 mr = 2124 m= 0 mr = 7 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1867 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 5193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5329853E-10 5.6808702E-10 midg,1,midg; midg,igrid,midg 1.4298226E-09 -5.0845572E-10 1,midg,midg; igrid,midg,midg -5.9008610E-11 9.6125663E-10 gauss-seidel spectral radius is 0.9833330 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 13:25:09 rms-change max change #iterations 6.3517965E-02 15.16008 at 10iterations 4.5012152E-03 0.8720493 at 20iterations 3.1358461E-04 5.8436394E-02 at 30iterations 2.1523992E-05 3.9844513E-03 at 40iterations 1.5197743E-06 2.7847290E-04 at 50iterations finished qdiffx linear iterations at : 13:25:12 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 1.5197743E-06 2.7847290E-04 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 13:25:13 3.658u 0.214s 0:04.43 87.1% 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 13:25:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.672801 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 1.672801 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1943 total number of charged atoms : 1813 net assigned charge : 5.000010 assigned positive charge : 284.3641 centred at (gu) : 89.20570 90.15025 87.61915 assigned negative charge : -279.3644 centred at (gu) : 88.95271 90.60812 87.52753 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 44992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17910 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15121 mr = 30018 m= 1879 mr = 10929 m= 62 mr = 1035 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 222 time to turn everything in is 0.2300000 number of dielectric boundary points 20068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 13999 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) : 0.5576004 object centre at (A) : -11.41050 20.60050 29.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0318147E-02 2.0194517E-02 midg,1,midg; midg,igrid,midg 6.0256948E-03 -4.8251641E-03 1,midg,midg; igrid,midg,midg -9.2028786E-04 1.3585747E-03 gauss-seidel spectral radius is 0.9981583 estimated iterations to convergence 185 setup time was (sec) 0.4600000 now iterating at: 13:25:14 rms-change max change #iterations 2.707744 168.9981 at 10iterations 1.113317 52.50065 at 20iterations 0.4591620 21.05492 at 30iterations 0.1904920 8.030684 at 40iterations 7.8644179E-02 3.501302 at 50iterations 3.2781135E-02 1.362051 at 60iterations 1.3580719E-02 0.6134968 at 70iterations 5.5931211E-03 0.2518940 at 80iterations 2.3055642E-03 0.1070366 at 90iterations 9.6475217E-04 3.8181901E-02 at 100iterations 3.9778155E-04 1.8848419E-02 at 110iterations 1.6504970E-04 7.2040558E-03 at 120iterations finished qdiffx linear iterations at : 13:25:23 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.6504970E-04 7.2040558E-03 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 13:25:23 7.979u 0.261s 0:10.48 78.5% 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 Sat Oct 15 2011 at 13:25:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.509202 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 2.509202 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1943 total number of charged atoms : 1813 net assigned charge : 5.000010 assigned positive charge : 284.3641 centred at (gu) : 88.80862 90.22547 86.42862 assigned negative charge : -279.3644 centred at (gu) : 88.42901 90.91212 86.29119 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 104216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17910 grid for indexing accessible points = 1.400000 m= 50519 mr = 73160 m= 16376 mr = 40712 m= 3042 mr = 13030 m= 268 mr = 2109 m= 4 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 0.6000000 number of dielectric boundary points 45285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 14494 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) : 1.672801 object centre at (A) : -11.41050 20.60050 29.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2615039 0.2106793 midg,1,midg; midg,igrid,midg 6.4836606E-02 -7.9776987E-02 1,midg,midg; igrid,midg,midg -2.9111013E-02 1.8067032E-02 gauss-seidel spectral radius is 0.9990981 estimated iterations to convergence 263 setup time was (sec) 0.8400000 now iterating at: 13:25:24 rms-change max change #iterations 6.759614 352.4298 at 10iterations 3.685706 99.17160 at 20iterations 1.997889 50.27216 at 30iterations 1.083640 25.72390 at 40iterations 0.5872476 14.91949 at 50iterations 0.3188442 8.156400 at 60iterations 0.1726706 3.955484 at 70iterations 9.3452759E-02 2.183960 at 80iterations 5.0417792E-02 1.219345 at 90iterations 2.7323648E-02 0.7236128 at 100iterations 1.4752259E-02 0.3474617 at 110iterations 8.0080936E-03 0.1900005 at 120iterations 4.3143560E-03 9.7636700E-02 at 130iterations 2.3383009E-03 5.7259083E-02 at 140iterations 1.2624844E-03 3.2284737E-02 at 150iterations 6.8198581E-04 1.5362263E-02 at 160iterations 3.6865284E-04 9.7098351E-03 at 170iterations 1.9932097E-04 4.7340393E-03 at 180iterations finished qdiffx linear iterations at : 13:25:39 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 1.9932097E-04 4.7340393E-03 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 13:25:39 12.564u 0.252s 0:15.68 81.6% 0+0k 0+0io 0pf+0w