Mon Oct 10 13:56:32 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 Mon Oct 10 2011 at 13:56:32 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: HIR 441 has a net charge of 0.5140 !!! WARNING: HIR 445 has a net charge of 0.5140 !!! WARNING: HIR 451 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6381758 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): 16.94400 72.72800 ymin,ymax (A): 14.37300 63.50200 zmin,zma (A): 20.75900 65.25400 x,y,z range (A): 55.78400 49.12901 44.49500 scale (grids/A): 0.6381758 object centre (A): 44.83600 38.93750 43.00650 number of atom coordinates read : 2579 total number of charged atoms : 2439 net assigned charge : -1.957992 assigned positive charge : 400.0460 centred at (gu) : 91.18627 91.03718 91.63864 assigned negative charge : -402.0044 centred at (gu) : 91.19305 90.84890 91.70092 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6911 nv = 96 ne = 84 npr = 52328 no. pairs analyzed = 52328 no. exposed pairs = 3135 no. arc points = 23146 no. surface atoms = 1057 nbur = 1522 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3680 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3000000 number of dielectric boundary points 3568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2298 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9778391E-09 -1.4211289E-08 midg,1,midg; midg,igrid,midg -1.9775070E-08 2.3049568E-08 1,midg,midg; igrid,midg,midg -1.5750562E-09 -4.5614614E-09 gauss-seidel spectral radius is 0.9872784 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 13:56:33 rms-change max change #iterations 0.1470251 23.26598 at 10iterations 1.4389589E-02 2.365337 at 20iterations 1.3985268E-03 0.2174664 at 30iterations 1.3936599E-04 2.2984743E-02 at 40iterations 1.3774943E-05 2.1333694E-03 at 50iterations finished qdiffx linear iterations at : 13:56:37 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.3774943E-05 2.1333694E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 13:56:37 4.459u 0.407s 0:05.14 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 Mon Oct 10 2011 at 13:56:37 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: HIR 441 has a net charge of 0.5140 !!! WARNING: HIR 445 has a net charge of 0.5140 !!! WARNING: HIR 451 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.914528 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): 16.94400 72.72800 ymin,ymax (A): 14.37300 63.50200 zmin,zma (A): 20.75900 65.25400 x,y,z range (A): 55.78400 49.12901 44.49500 scale (grids/A): 1.914528 object centre (A): 44.83600 38.93750 43.00650 number of atom coordinates read : 2579 total number of charged atoms : 2439 net assigned charge : -1.957992 assigned positive charge : 400.0460 centred at (gu) : 93.55851 93.11111 94.91534 assigned negative charge : -402.0044 centred at (gu) : 93.57883 92.54658 95.10257 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74911 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23146 grid for indexing accessible points = 1.400000 m= 25307 mr = 50973 m= 3951 mr = 18413 m= 257 mr = 2418 m= 4 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3820 time to turn everything in is 0.5900000 number of dielectric boundary points 32515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19195 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) : 0.6381758 object centre at (A) : 44.83600 38.93750 43.00650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0391758E-03 -2.0301156E-02 midg,1,midg; midg,igrid,midg -1.6008047E-02 1.2469850E-02 1,midg,midg; igrid,midg,midg 9.3553346E-03 -3.1495921E-02 gauss-seidel spectral radius is 0.9986476 estimated iterations to convergence 215 setup time was (sec) 0.9300000 now iterating at: 13:56:39 rms-change max change #iterations 4.396571 186.3690 at 10iterations 2.066104 70.27423 at 20iterations 0.9669920 32.25940 at 30iterations 0.4536546 15.14120 at 40iterations 0.2129859 7.596153 at 50iterations 9.9713050E-02 2.975509 at 60iterations 4.7040913E-02 1.492711 at 70iterations 2.2031451E-02 0.8048859 at 80iterations 1.0349904E-02 0.3147907 at 90iterations 4.8664254E-03 0.1454005 at 100iterations 2.2842493E-03 7.0901871E-02 at 110iterations 1.0757956E-03 3.6747456E-02 at 120iterations finished qdiffx linear iterations at : 13:56:49 total time elapsed so far: 10.75000 # loops : 120 mean,max change (kT/e) : 1.0757956E-03 3.6747456E-02 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.91000 DelPhi exited at 13:56:49 10.918u 0.460s 0:11.67 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 Mon Oct 10 2011 at 13:56:49 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: HIR 441 has a net charge of 0.5140 !!! WARNING: HIR 445 has a net charge of 0.5140 !!! WARNING: HIR 451 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.871791 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): 16.94400 72.72800 ymin,ymax (A): 14.37300 63.50200 zmin,zma (A): 20.75900 65.25400 x,y,z range (A): 55.78400 49.12901 44.49500 scale (grids/A): 2.871791 object centre (A): 44.83600 38.93750 43.00650 number of atom coordinates read : 2579 total number of charged atoms : 2439 net assigned charge : -1.957992 assigned positive charge : 400.0460 centred at (gu) : 95.33771 94.66658 97.37309 assigned negative charge : -402.0044 centred at (gu) : 95.36809 93.81976 97.65374 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 173288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23146 grid for indexing accessible points = 1.400000 m= 83334 mr = 123991 m= 28991 mr = 67513 m= 7133 mr = 23030 m= 1137 mr = 5320 m= 88 mr = 778 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 12839 time to turn everything in is 1.560000 number of dielectric boundary points 73294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 19509 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) : 1.914528 object centre at (A) : 44.83600 38.93750 43.00650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1540958E-02 -0.3909845 midg,1,midg; midg,igrid,midg -0.1319854 0.1482126 1,midg,midg; igrid,midg,midg 0.2097554 -0.1678384 gauss-seidel spectral radius is 0.9992583 estimated iterations to convergence 290 setup time was (sec) 1.880000 now iterating at: 13:56:51 rms-change max change #iterations 10.17353 415.3671 at 10iterations 5.893436 138.1201 at 20iterations 3.386672 63.43663 at 30iterations 1.943805 36.62466 at 40iterations 1.117464 22.01842 at 50iterations 0.6399174 11.69939 at 60iterations 0.3665700 7.549306 at 70iterations 0.2102148 3.814957 at 80iterations 0.1205595 2.304173 at 90iterations 6.9028847E-02 1.334616 at 100iterations 3.9468724E-02 0.7203865 at 110iterations 2.2627307E-02 0.3789525 at 120iterations 1.3004515E-02 0.2381009 at 130iterations 7.4352245E-03 0.1542931 at 140iterations 4.2708889E-03 8.2455635E-02 at 150iterations 2.4473725E-03 4.4601440E-02 at 160iterations 1.4016248E-03 2.6084900E-02 at 170iterations 8.0488413E-04 1.5713215E-02 at 180iterations finished qdiffx linear iterations at : 13:57:07 total time elapsed so far: 17.59000 # loops : 180 mean,max change (kT/e) : 8.0488413E-04 1.5713215E-02 energy calculations done at 17.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.76000 DelPhi exited at 13:57:08 17.760u 0.469s 0:18.89 96.4% 0+0k 0+0io 0pf+0w