Sat Oct 8 14:54:15 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 14:54:16 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6388744 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): -12.16600 43.55700 ymin,ymax (A): -23.21100 22.50100 zmin,zma (A): -7.506000 47.12000 x,y,z range (A): 55.72300 45.71200 54.62600 scale (grids/A): 0.6388744 object centre (A): 15.69550 -0.3550005 19.80700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : -0.9859920 assigned positive charge : 454.6486 centred at (gu) : 88.84174 89.74452 91.75054 assigned negative charge : -455.6353 centred at (gu) : 88.80593 89.64468 91.69714 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8225 nv = 96 ne = 84 npr = 63413 no. pairs analyzed = 63413 no. exposed pairs = 3423 no. arc points = 24374 no. surface atoms = 1164 nbur = 1869 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 4828 m= 0 mr = 48 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2355 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10054 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8487082E-09 8.2935880E-09 midg,1,midg; midg,igrid,midg -1.5600493E-08 1.1005856E-08 1,midg,midg; igrid,midg,midg -7.9328659E-09 2.5536016E-09 gauss-seidel spectral radius is 0.9873395 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 14:54:16 rms-change max change #iterations 0.1554203 23.26590 at 10iterations 1.5696079E-02 2.347820 at 20iterations 1.6105071E-03 0.2121906 at 30iterations 1.9206751E-04 2.9113770E-02 at 40iterations 2.7476561E-05 4.1389465E-03 at 50iterations finished qdiffx linear iterations at : 14:54:20 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 2.7476561E-05 4.1389465E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 14:54:20 4.291u 0.235s 0:04.83 93.5% 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 14:54:20 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.916623 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): -12.16600 43.55700 ymin,ymax (A): -23.21100 22.50100 zmin,zma (A): -7.506000 47.12000 x,y,z range (A): 55.72300 45.71200 54.62600 scale (grids/A): 1.916623 object centre (A): 15.69550 -0.3550005 19.80700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : -0.9859920 assigned positive charge : 454.6486 centred at (gu) : 86.52477 89.23283 95.25106 assigned negative charge : -455.6353 centred at (gu) : 86.41748 88.93374 95.09125 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24374 grid for indexing accessible points = 1.400000 m= 32335 mr = 64901 m= 4752 mr = 24349 m= 289 mr = 2950 m= 0 mr = 116 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 380 time to turn everything in is 0.6600000 number of dielectric boundary points 34811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 22745 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) : 0.6388744 object centre at (A) : 15.69550 -0.3550005 19.80700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9263320E-02 7.5769508E-03 midg,1,midg; midg,igrid,midg -2.3190391E-03 2.1534245E-02 1,midg,midg; igrid,midg,midg -3.3708159E-02 6.4027300E-03 gauss-seidel spectral radius is 0.9986869 estimated iterations to convergence 219 setup time was (sec) 0.9800000 now iterating at: 14:54:22 rms-change max change #iterations 4.717556 182.2716 at 10iterations 2.251566 71.91579 at 20iterations 1.071949 32.73932 at 30iterations 0.5087436 14.78703 at 40iterations 0.2425619 7.313131 at 50iterations 0.1153262 3.245743 at 60iterations 5.5000383E-02 1.610245 at 70iterations 2.6201585E-02 0.8639832 at 80iterations 1.2479537E-02 0.3632164 at 90iterations 5.9484500E-03 0.1777248 at 100iterations 2.8297333E-03 9.4897747E-02 at 110iterations 1.3513920E-03 4.1563034E-02 at 120iterations finished qdiffx linear iterations at : 14:54:30 total time elapsed so far: 9.690000 # loops : 120 mean,max change (kT/e) : 1.3513920E-03 4.1563034E-02 energy calculations done at 9.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.870000 DelPhi exited at 14:54:31 9.869u 0.287s 0:10.54 96.2% 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 14:54:31 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.874935 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): -12.16600 43.55700 ymin,ymax (A): -23.21100 22.50100 zmin,zma (A): -7.506000 47.12000 x,y,z range (A): 55.72300 45.71200 54.62600 scale (grids/A): 2.874935 object centre (A): 15.69550 -0.3550005 19.80700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : -0.9859920 assigned positive charge : 454.6486 centred at (gu) : 84.78693 88.84928 97.87638 assigned negative charge : -455.6353 centred at (gu) : 84.62627 88.40055 97.63686 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 207929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24374 grid for indexing accessible points = 1.400000 m= 106409 mr = 156697 m= 37162 mr = 88899 m= 8637 mr = 30063 m= 1279 mr = 6417 m= 62 mr = 849 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 1198 time to turn everything in is 1.680000 number of dielectric boundary points 78530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 23084 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) : 1.916623 object centre at (A) : 15.69550 -0.3550005 19.80700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6368268E-02 0.2497414 midg,1,midg; midg,igrid,midg -1.4643296E-02 0.2592620 1,midg,midg; igrid,midg,midg -0.5322244 0.1484579 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 2.030000 now iterating at: 14:54:33 rms-change max change #iterations 10.94002 449.1946 at 10iterations 6.412570 125.1126 at 20iterations 3.737929 65.07172 at 30iterations 2.177490 38.21992 at 40iterations 1.263784 23.65639 at 50iterations 0.7343174 12.74128 at 60iterations 0.4264471 7.244464 at 70iterations 0.2469081 4.212540 at 80iterations 0.1430614 2.305883 at 90iterations 8.2872361E-02 1.533201 at 100iterations 4.8018456E-02 0.8520451 at 110iterations 2.7798282E-02 0.4552231 at 120iterations 1.6100777E-02 0.2686749 at 130iterations 9.3279388E-03 0.1529388 at 140iterations 5.4110591E-03 9.1735840E-02 at 150iterations 3.1374632E-03 5.4858208E-02 at 160iterations 1.8269145E-03 2.9872894E-02 at 170iterations 1.0695979E-03 1.9007683E-02 at 180iterations finished qdiffx linear iterations at : 14:54:47 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 1.0695979E-03 1.9007683E-02 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.95000 DelPhi exited at 14:54:47 15.951u 0.301s 0:16.51 98.4% 0+0k 0+0io 0pf+0w