Sun Oct 9 10:57:21 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 10:57:21 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 = 2585 !!! WARNING: HIR 211 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6132116 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): -20.64000 37.41500 ymin,ymax (A): 18.79700 70.67000 zmin,zma (A): 30.79400 88.35201 x,y,z range (A): 58.05500 51.87300 57.55801 scale (grids/A): 0.6132116 object centre (A): 8.387499 44.73350 59.57300 number of atom coordinates read : 2585 total number of charged atoms : 2443 net assigned charge : -3.485987 assigned positive charge : 373.2526 centred at (gu) : 90.02557 88.44750 91.27888 assigned negative charge : -376.7398 centred at (gu) : 90.11349 88.52592 91.47575 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6750 nv = 96 ne = 84 npr = 51392 no. pairs analyzed = 51392 no. exposed pairs = 3496 no. arc points = 25154 no. surface atoms = 1183 nbur = 1402 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 349 mr = 3452 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2800000 number of dielectric boundary points 3611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2345 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8108 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9460774E-09 -1.7062973E-08 midg,1,midg; midg,igrid,midg 2.7944436E-09 -4.4993289E-09 1,midg,midg; igrid,midg,midg 2.3937845E-09 -6.8857333E-09 gauss-seidel spectral radius is 0.9862443 estimated iterations to convergence 70 setup time was (sec) 0.5000000 now iterating at: 10:57:22 rms-change max change #iterations 0.1187280 19.43080 at 10iterations 1.0411479E-02 1.863558 at 20iterations 9.2876022E-04 0.1537895 at 30iterations 8.7931177E-05 1.4530182E-02 at 40iterations 1.2018072E-05 2.2239685E-03 at 50iterations finished qdiffx linear iterations at : 10:57:24 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.2018072E-05 2.2239685E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 10:57:25 3.123u 0.139s 0:03.66 88.7% 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 Sun Oct 9 2011 at 10:57:25 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 = 2585 !!! WARNING: HIR 211 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.839635 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): -20.64000 37.41500 ymin,ymax (A): 18.79700 70.67000 zmin,zma (A): 30.79400 88.35201 x,y,z range (A): 58.05500 51.87300 57.55801 scale (grids/A): 1.839635 object centre (A): 8.387499 44.73350 59.57300 number of atom coordinates read : 2585 total number of charged atoms : 2443 net assigned charge : -3.485987 assigned positive charge : 373.2526 centred at (gu) : 90.07584 85.34224 93.83582 assigned negative charge : -376.7398 centred at (gu) : 90.34039 85.57740 94.42714 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25154 grid for indexing accessible points = 1.400000 m= 24632 mr = 48730 m= 3849 mr = 17159 m= 211 mr = 2237 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 33480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19137 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) : 0.6132116 object centre at (A) : 8.387499 44.73350 59.57300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9163987E-02 -3.9698485E-02 midg,1,midg; midg,igrid,midg 1.3898538E-02 -8.5011311E-03 1,midg,midg; igrid,midg,midg -2.0156886E-02 -2.5916487E-02 gauss-seidel spectral radius is 0.9985610 estimated iterations to convergence 209 setup time was (sec) 0.8100000 now iterating at: 10:57:26 rms-change max change #iterations 3.923826 171.8296 at 10iterations 1.787976 68.94238 at 20iterations 0.8184205 26.37785 at 30iterations 0.3739492 11.92175 at 40iterations 0.1712006 5.731227 at 50iterations 7.8676686E-02 2.983991 at 60iterations 3.6068093E-02 1.109310 at 70iterations 1.6511621E-02 0.5247803 at 80iterations 7.5808391E-03 0.2526436 at 90iterations 3.4761389E-03 0.1184921 at 100iterations 1.5966423E-03 5.2332878E-02 at 110iterations 7.3282380E-04 2.3394108E-02 at 120iterations finished qdiffx linear iterations at : 10:57:32 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 7.3282380E-04 2.3394108E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 10:57:33 6.943u 0.162s 0:07.41 95.8% 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 10:57:33 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 = 2585 !!! WARNING: HIR 211 has a net charge of 0.5140 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: 2.759452 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): -20.64000 37.41500 ymin,ymax (A): 18.79700 70.67000 zmin,zma (A): 30.79400 88.35201 x,y,z range (A): 58.05500 51.87300 57.55801 scale (grids/A): 2.759452 object centre (A): 8.387499 44.73350 59.57300 number of atom coordinates read : 2585 total number of charged atoms : 2443 net assigned charge : -3.485987 assigned positive charge : 373.2526 centred at (gu) : 90.11358 83.01307 95.75349 assigned negative charge : -376.7398 centred at (gu) : 90.51054 83.36610 96.64082 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 169061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25154 grid for indexing accessible points = 1.400000 m= 80043 mr = 118939 m= 28108 mr = 63260 m= 6830 mr = 21841 m= 895 mr = 4856 m= 32 mr = 509 m= 0 mr = 4 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 75560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 19541 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) : 1.839635 object centre at (A) : 8.387499 44.73350 59.57300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2280462 -0.1167318 midg,1,midg; midg,igrid,midg 0.2114045 -0.1434415 1,midg,midg; igrid,midg,midg -0.3382478 -0.2504854 gauss-seidel spectral radius is 0.9992470 estimated iterations to convergence 288 setup time was (sec) 1.530000 now iterating at: 10:57:34 rms-change max change #iterations 9.502674 268.7802 at 10iterations 5.592037 149.3631 at 20iterations 3.256466 70.48662 at 30iterations 1.892483 37.33351 at 40iterations 1.091371 22.70768 at 50iterations 0.6303228 12.59093 at 60iterations 0.3620913 7.446926 at 70iterations 0.2078657 3.962190 at 80iterations 0.1193080 2.341408 at 90iterations 6.8495318E-02 1.332729 at 100iterations 3.9148431E-02 0.7098465 at 110iterations 2.2471763E-02 0.4677887 at 120iterations 1.2847821E-02 0.2552185 at 130iterations 7.3392522E-03 0.1388760 at 140iterations 4.1986937E-03 7.4855804E-02 at 150iterations 2.4081005E-03 4.4005394E-02 at 160iterations 1.3767028E-03 2.4353027E-02 at 170iterations 7.9051632E-04 1.4057159E-02 at 180iterations finished qdiffx linear iterations at : 10:57:44 total time elapsed so far: 10.82000 # loops : 180 mean,max change (kT/e) : 7.9051632E-04 1.4057159E-02 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 10:57:44 11.021u 0.184s 0:11.61 96.4% 0+0k 0+0io 0pf+0w