Sat Oct 8 17:40:00 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 Sat Oct 8 2011 at 17:40:00 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5223464 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): -1.258000 44.51400 ymin,ymax (A): -30.64900 26.29100 zmin,zma (A): 0.9220001 69.07600 x,y,z range (A): 45.77200 56.94000 68.15401 scale (grids/A): 0.5223464 object centre (A): 21.62800 -2.179000 34.99900 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.871982 assigned positive charge : 540.6540 centred at (gu) : 90.43950 91.65965 90.75531 assigned negative charge : -546.5279 centred at (gu) : 90.40309 91.61489 90.75889 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6074 nv = 96 ne = 84 npr = 71983 no. pairs analyzed = 71983 no. exposed pairs = 4276 no. arc points = 29180 no. surface atoms = 1451 nbur = 2076 mkacc time = 0.2100000 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 = 1.652000 m= 216 mr = 3228 m= 1 mr = 9 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 0.4300000 number of dielectric boundary points 3054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2922 ## 416 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0790743E-10 -1.8557070E-10 midg,1,midg; midg,igrid,midg -1.8843639E-10 7.3509428E-12 1,midg,midg; igrid,midg,midg -2.3236929E-10 -2.6897692E-11 gauss-seidel spectral radius is 0.9811570 estimated iterations to convergence 60 setup time was (sec) 0.7000000 now iterating at: 17:40:01 rms-change max change #iterations 6.6801168E-02 11.23442 at 10iterations 4.0221349E-03 0.7656317 at 20iterations 3.2349103E-04 5.5374146E-02 at 30iterations 5.6583402E-05 9.5405579E-03 at 40iterations 1.3382518E-05 2.2602081E-03 at 50iterations finished qdiffx linear iterations at : 17:40:05 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.3382518E-05 2.2602081E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 17:40:05 4.262u 0.276s 0:04.80 94.3% 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 17:40:05 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.567039 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): -1.258000 44.51400 ymin,ymax (A): -30.64900 26.29100 zmin,zma (A): 0.9220001 69.07600 x,y,z range (A): 45.77200 56.94000 68.15401 scale (grids/A): 1.567039 object centre (A): 21.62800 -2.179000 34.99900 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.871982 assigned positive charge : 540.6540 centred at (gu) : 91.31748 94.97794 92.26495 assigned negative charge : -546.5279 centred at (gu) : 91.20898 94.84442 92.27628 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29180 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20538 mr = 47996 m= 1789 mr = 13955 m= 41 mr = 747 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.6300000 number of dielectric boundary points 28446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 444 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 25571 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) : 0.5223464 object centre at (A) : 21.62800 -2.179000 34.99900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7192204E-03 8.8605508E-03 midg,1,midg; midg,igrid,midg -8.0919135E-03 -1.0593540E-02 1,midg,midg; igrid,midg,midg -4.2234254E-03 1.3180252E-03 gauss-seidel spectral radius is 0.9980642 estimated iterations to convergence 181 setup time was (sec) 0.9200000 now iterating at: 17:40:06 rms-change max change #iterations 3.400743 147.5923 at 10iterations 1.377135 53.92750 at 20iterations 0.5586139 18.45342 at 30iterations 0.2274342 8.679884 at 40iterations 9.2150249E-02 3.334171 at 50iterations 3.7457753E-02 1.372054 at 60iterations 1.5232070E-02 0.5700302 at 70iterations 6.1959354E-03 0.2783880 at 80iterations 2.5347560E-03 9.0051651E-02 at 90iterations 1.0486881E-03 4.0352821E-02 at 100iterations 4.4785498E-04 1.5007019E-02 at 110iterations 2.0093964E-04 8.0578923E-03 at 120iterations finished qdiffx linear iterations at : 17:40:15 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 2.0093964E-04 8.0578923E-03 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 17:40:15 9.535u 0.341s 0:10.13 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 17:40:15 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.350559 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): -1.258000 44.51400 ymin,ymax (A): -30.64900 26.29100 zmin,zma (A): 0.9220001 69.07600 x,y,z range (A): 45.77200 56.94000 68.15401 scale (grids/A): 2.350559 object centre (A): 21.62800 -2.179000 34.99900 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.871982 assigned positive charge : 540.6540 centred at (gu) : 91.97570 97.46644 93.39717 assigned negative charge : -546.5279 centred at (gu) : 91.81347 97.26653 93.41431 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 160154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29180 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 73107 mr = 117478 m= 18904 mr = 57858 m= 2529 mr = 13773 m= 107 mr = 1480 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 1.500000 number of dielectric boundary points 64192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 26976 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) : 1.567039 object centre at (A) : 21.62800 -2.179000 34.99900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1682005 8.1126364E-03 midg,1,midg; midg,igrid,midg -0.1149437 -0.1599227 1,midg,midg; igrid,midg,midg -7.2458349E-02 4.4871572E-02 gauss-seidel spectral radius is 0.9991049 estimated iterations to convergence 264 setup time was (sec) 1.830000 now iterating at: 17:40:17 rms-change max change #iterations 9.053131 293.8198 at 10iterations 5.025955 130.9085 at 20iterations 2.773630 62.72057 at 30iterations 1.521225 32.14694 at 40iterations 0.8352963 19.64282 at 50iterations 0.4561108 9.722863 at 60iterations 0.2496495 5.261542 at 70iterations 0.1358054 2.827096 at 80iterations 7.3849037E-02 1.494141 at 90iterations 4.0171124E-02 0.8787117 at 100iterations 2.1872262E-02 0.4497067 at 110iterations 1.1929943E-02 0.2336636 at 120iterations 6.4710411E-03 0.1334009 at 130iterations 3.5139369E-03 7.0247650E-02 at 140iterations 1.9213399E-03 4.3403625E-02 at 150iterations 1.0530580E-03 2.2094727E-02 at 160iterations 5.7802140E-04 1.4371872E-02 at 170iterations 3.2061414E-04 6.5715313E-03 at 180iterations finished qdiffx linear iterations at : 17:40:31 total time elapsed so far: 15.73000 # loops : 180 mean,max change (kT/e) : 3.2061414E-04 6.5715313E-03 energy calculations done at 15.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.92000 DelPhi exited at 17:40:32 15.918u 0.336s 0:16.57 98.0% 0+0k 0+0io 0pf+0w