Sat Oct 8 20:46:51 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 20:46:51 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 = 2577 !!! 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: ZN4 427 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6213239 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): -10.82200 38.64300 ymin,ymax (A): -22.24500 24.50500 zmin,zma (A): -12.60000 44.69700 x,y,z range (A): 49.46500 46.75000 57.29700 scale (grids/A): 0.6213239 object centre (A): 13.91050 1.130000 16.04850 number of atom coordinates read : 2577 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.58700 89.39188 89.82411 assigned negative charge : -387.4045 centred at (gu) : 88.49106 89.44060 89.69867 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6606 nv = 96 ne = 84 npr = 53304 no. pairs analyzed = 53304 no. exposed pairs = 2980 no. arc points = 21228 no. surface atoms = 1003 nbur = 1574 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 3725 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 94 time to turn everything in is 0.3400000 number of dielectric boundary points 3142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2189 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5155662E-09 1.1505987E-08 midg,1,midg; midg,igrid,midg 7.7539060E-09 9.5607453E-11 1,midg,midg; igrid,midg,midg -4.5051856E-09 7.3331359E-09 gauss-seidel spectral radius is 0.9865795 estimated iterations to convergence 71 setup time was (sec) 0.6000000 now iterating at: 20:46:52 rms-change max change #iterations 0.1276841 20.25527 at 10iterations 1.1774666E-02 1.775086 at 20iterations 1.0980516E-03 0.1600151 at 30iterations 1.0131067E-04 1.5724182E-02 at 40iterations 9.4839570E-06 1.4705658E-03 at 50iterations finished qdiffx linear iterations at : 20:46:56 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 9.4839570E-06 1.4705658E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 20:46:56 4.054u 0.277s 0:04.60 93.9% 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 Sat Oct 8 2011 at 20:46:56 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 = 2577 !!! 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: ZN4 427 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.863972 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): -10.82200 38.64300 ymin,ymax (A): -22.24500 24.50500 zmin,zma (A): -12.60000 44.69700 x,y,z range (A): 49.46500 46.75000 57.29700 scale (grids/A): 1.863972 object centre (A): 13.91050 1.130000 16.04850 number of atom coordinates read : 2577 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.76064 88.17503 89.47207 assigned negative charge : -387.4045 centred at (gu) : 85.47284 88.32170 89.09589 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21228 grid for indexing accessible points = 1.400000 m= 25026 mr = 50725 m= 3305 mr = 18596 m= 167 mr = 2013 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 4166 time to turn everything in is 0.6300000 number of dielectric boundary points 28972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19240 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) : 0.6213239 object centre at (A) : 13.91050 1.130000 16.04850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5915271E-02 2.1198936E-02 midg,1,midg; midg,igrid,midg 1.2384384E-02 1.1498266E-03 1,midg,midg; igrid,midg,midg -3.7978168E-03 3.2901749E-02 gauss-seidel spectral radius is 0.9985707 estimated iterations to convergence 210 setup time was (sec) 0.9200000 now iterating at: 20:46:57 rms-change max change #iterations 4.057967 193.1297 at 10iterations 1.863795 59.63630 at 20iterations 0.8587238 28.33141 at 30iterations 0.3953505 14.20535 at 40iterations 0.1820733 6.061654 at 50iterations 8.3692938E-02 3.177780 at 60iterations 3.8572568E-02 1.262739 at 70iterations 1.7730867E-02 0.6042786 at 80iterations 8.1744147E-03 0.2658081 at 90iterations 3.7656685E-03 0.1302826 at 100iterations 1.7288878E-03 5.7014465E-02 at 110iterations 7.9861435E-04 2.6493073E-02 at 120iterations finished qdiffx linear iterations at : 20:47:05 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 7.9861435E-04 2.6493073E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 20:47:06 9.320u 0.312s 0:09.89 97.3% 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 Sat Oct 8 2011 at 20:47:06 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 = 2577 !!! 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: ZN4 427 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.795958 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): -10.82200 38.64300 ymin,ymax (A): -22.24500 24.50500 zmin,zma (A): -12.60000 44.69700 x,y,z range (A): 49.46500 46.75000 57.29700 scale (grids/A): 2.795958 object centre (A): 13.91050 1.130000 16.04850 number of atom coordinates read : 2577 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.64100 87.26242 89.20797 assigned negative charge : -387.4045 centred at (gu) : 83.20915 87.48254 88.64367 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 166029 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21228 grid for indexing accessible points = 1.400000 m= 83461 mr = 122203 m= 27592 mr = 69076 m= 5851 mr = 22168 m= 695 mr = 4352 m= 39 mr = 464 m= 0 mr = 16 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 14542 time to turn everything in is 1.580000 number of dielectric boundary points 65388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 19627 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) : 1.863972 object centre at (A) : 13.91050 1.130000 16.04850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8600895E-02 0.2650576 midg,1,midg; midg,igrid,midg 0.1542237 2.6625942E-03 1,midg,midg; igrid,midg,midg -3.9173976E-02 0.4366008 gauss-seidel spectral radius is 0.9992343 estimated iterations to convergence 285 setup time was (sec) 1.900000 now iterating at: 20:47:08 rms-change max change #iterations 9.442320 303.0407 at 10iterations 5.407375 102.2944 at 20iterations 3.080666 57.63179 at 30iterations 1.756659 34.69894 at 40iterations 1.001112 18.88322 at 50iterations 0.5684285 10.97719 at 60iterations 0.3242323 6.427582 at 70iterations 0.1844107 3.259833 at 80iterations 0.1048083 2.062504 at 90iterations 5.9550479E-02 1.055979 at 100iterations 3.3707578E-02 0.5974846 at 110iterations 1.9258682E-02 0.3760611 at 120iterations 1.0958617E-02 0.2039070 at 130iterations 6.2094904E-03 0.1125126 at 140iterations 3.5305840E-03 6.5254211E-02 at 150iterations 2.0057210E-03 3.6436081E-02 at 160iterations 1.1439308E-03 2.3528099E-02 at 170iterations 6.4888143E-04 1.2362719E-02 at 180iterations finished qdiffx linear iterations at : 20:47:22 total time elapsed so far: 15.36000 # loops : 180 mean,max change (kT/e) : 6.4888143E-04 1.2362719E-02 energy calculations done at 15.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 20:47:22 15.537u 0.315s 0:16.12 98.2% 0+0k 0+0io 0pf+0w