Sat Oct 8 19:00:24 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 8 2011 at 19:00:24 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6308701 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): -31.86200 17.51200 ymin,ymax (A): -23.78600 23.23900 zmin,zma (A): -12.51500 43.91500 x,y,z range (A): 49.37400 47.02500 56.43000 scale (grids/A): 0.6308701 object centre (A): -7.174999 -0.2734995 15.70000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.53145 89.19238 89.95214 assigned negative charge : -388.8955 centred at (gu) : 88.42233 89.23895 89.84026 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6826 nv = 96 ne = 84 npr = 54746 no. pairs analyzed = 54746 no. exposed pairs = 2973 no. arc points = 21612 no. surface atoms = 998 nbur = 1608 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3860 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 281 time to turn everything in is 0.3100000 number of dielectric boundary points 3242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2167 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8328 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1627280E-09 1.5000037E-08 midg,1,midg; midg,igrid,midg 1.1125595E-08 8.0385554E-10 1,midg,midg; igrid,midg,midg -6.8554975E-09 1.0873666E-08 gauss-seidel spectral radius is 0.9869813 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 19:00:25 rms-change max change #iterations 0.1379045 19.47381 at 10iterations 1.3258794E-02 2.219448 at 20iterations 1.2901981E-03 0.1856842 at 30iterations 1.2161452E-04 1.8959045E-02 at 40iterations 1.1987228E-05 1.7213821E-03 at 50iterations finished qdiffx linear iterations at : 19:00:29 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 1.1987228E-05 1.7213821E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 19:00:29 4.418u 0.431s 0:05.11 94.7% 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 8 2011 at 19:00:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.892610 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): -31.86200 17.51200 ymin,ymax (A): -23.78600 23.23900 zmin,zma (A): -12.51500 43.91500 x,y,z range (A): 49.37400 47.02500 56.43000 scale (grids/A): 1.892610 object centre (A): -7.174999 -0.2734995 15.70000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.59364 87.57683 89.85612 assigned negative charge : -388.8955 centred at (gu) : 85.26667 87.71655 89.52074 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21612 grid for indexing accessible points = 1.400000 m= 26326 mr = 51959 m= 3978 mr = 19733 m= 219 mr = 2543 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 8411 time to turn everything in is 0.6000000 number of dielectric boundary points 30069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19385 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) : 0.6308701 object centre at (A) : -7.174999 -0.2734995 15.70000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7926356E-02 2.8052052E-02 midg,1,midg; midg,igrid,midg 1.6505420E-02 1.7415241E-03 1,midg,midg; igrid,midg,midg -4.0329630E-03 3.9513074E-02 gauss-seidel spectral radius is 0.9986143 estimated iterations to convergence 213 setup time was (sec) 0.9500000 now iterating at: 19:00:31 rms-change max change #iterations 4.127141 167.8608 at 10iterations 1.926680 70.86799 at 20iterations 0.8973023 32.76273 at 30iterations 0.4159673 13.73552 at 40iterations 0.1943518 5.910465 at 50iterations 9.0798520E-02 3.001020 at 60iterations 4.2057723E-02 1.415554 at 70iterations 1.9642839E-02 0.6145546 at 80iterations 9.1781719E-03 0.2942896 at 90iterations 4.2564590E-03 0.1565619 at 100iterations 1.9840146E-03 6.5593719E-02 at 110iterations 9.2604518E-04 3.2318354E-02 at 120iterations finished qdiffx linear iterations at : 19:00:40 total time elapsed so far: 10.38000 # loops : 120 mean,max change (kT/e) : 9.2604518E-04 3.2318354E-02 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.55000 DelPhi exited at 19:00:41 10.554u 0.446s 0:11.28 97.4% 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 8 2011 at 19:00:41 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.838915 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): -31.86200 17.51200 ymin,ymax (A): -23.78600 23.23900 zmin,zma (A): -12.51500 43.91500 x,y,z range (A): 49.37400 47.02500 56.43000 scale (grids/A): 2.838915 object centre (A): -7.174999 -0.2734995 15.70000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.39027 86.36507 89.78413 assigned negative charge : -388.8955 centred at (gu) : 82.89988 86.57473 89.28101 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 170752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21612 grid for indexing accessible points = 1.400000 m= 85916 mr = 125261 m= 30358 mr = 71262 m= 7232 mr = 24651 m= 995 mr = 5526 m= 48 mr = 711 m= 0 mr = 16 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 28371 time to turn everything in is 1.550000 number of dielectric boundary points 67874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 19728 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) : 1.892610 object centre at (A) : -7.174999 -0.2734995 15.70000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1069684 0.3307172 midg,1,midg; midg,igrid,midg 0.2095991 1.7061168E-02 1,midg,midg; igrid,midg,midg -1.5946606E-02 0.4535853 gauss-seidel spectral radius is 0.9992446 estimated iterations to convergence 287 setup time was (sec) 1.870000 now iterating at: 19:00:43 rms-change max change #iterations 9.666764 368.8665 at 10iterations 5.567294 108.4015 at 20iterations 3.183343 62.51218 at 30iterations 1.816096 40.28838 at 40iterations 1.039796 21.79238 at 50iterations 0.5940437 11.39254 at 60iterations 0.3397746 5.859241 at 70iterations 0.1937746 3.588758 at 80iterations 0.1107147 2.191143 at 90iterations 6.3220210E-02 1.133415 at 100iterations 3.6101535E-02 0.7675238 at 110iterations 2.0614550E-02 0.3959742 at 120iterations 1.1739196E-02 0.2064724 at 130iterations 6.7170146E-03 0.1182885 at 140iterations 3.8349198E-03 6.7012787E-02 at 150iterations 2.1897801E-03 4.0534973E-02 at 160iterations 1.2488038E-03 2.3359299E-02 at 170iterations 7.1311457E-04 1.2775421E-02 at 180iterations finished qdiffx linear iterations at : 19:00:59 total time elapsed so far: 17.57000 # loops : 180 mean,max change (kT/e) : 7.1311457E-04 1.2775421E-02 energy calculations done at 17.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.73000 DelPhi exited at 19:00:59 17.739u 0.485s 0:18.49 98.4% 0+0k 0+0io 0pf+0w