Sun Oct 9 08:14:47 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 Sun Oct 9 2011 at 08:14:47 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 !!! WARNING: NAP 528 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5226839 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): 20.49900 88.60900 ymin,ymax (A): -7.435000 47.84500 zmin,zma (A): 23.44400 76.17700 x,y,z range (A): 68.11000 55.28000 52.73300 scale (grids/A): 0.5226839 object centre (A): 54.55400 20.20500 49.81050 number of atom coordinates read : 3277 total number of charged atoms : 3091 net assigned charge : 9.500010 assigned positive charge : 482.4337 centred at (gu) : 88.71682 90.66007 89.76501 assigned negative charge : -472.9351 centred at (gu) : 88.64618 90.66706 89.73850 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5735 nv = 96 ne = 84 npr = 66447 no. pairs analyzed = 66447 no. exposed pairs = 4109 no. arc points = 29095 no. surface atoms = 1373 nbur = 1904 mkacc time = 0.1400000 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 = 1.624000 m= 199 mr = 2943 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2763 ## 375 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6493513E-10 2.8852698E-10 midg,1,midg; midg,igrid,midg 2.1278397E-10 2.4932362E-10 1,midg,midg; igrid,midg,midg 3.5514744E-11 3.1041697E-10 gauss-seidel spectral radius is 0.9811714 estimated iterations to convergence 60 setup time was (sec) 0.5600000 now iterating at: 08:14:48 rms-change max change #iterations 6.0593706E-02 10.65892 at 10iterations 3.7290168E-03 0.5885248 at 20iterations 2.6936707E-04 4.2495728E-02 at 30iterations 3.3007054E-05 5.4950714E-03 at 40iterations 6.0061648E-06 8.2588196E-04 at 50iterations finished qdiffx linear iterations at : 08:14:50 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 6.0061648E-06 8.2588196E-04 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:14:51 3.320u 0.198s 0:03.79 92.6% 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 08:14:51 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 !!! WARNING: NAP 528 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.568052 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): 20.49900 88.60900 ymin,ymax (A): -7.435000 47.84500 zmin,zma (A): 23.44400 76.17700 x,y,z range (A): 68.11000 55.28000 52.73300 scale (grids/A): 1.568052 object centre (A): 54.55400 20.20500 49.81050 number of atom coordinates read : 3277 total number of charged atoms : 3091 net assigned charge : 9.500010 assigned positive charge : 482.4337 centred at (gu) : 86.14958 91.97939 89.29398 assigned negative charge : -472.9351 centred at (gu) : 85.93845 92.00085 89.21533 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29095 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18767 mr = 44226 m= 1719 mr = 12554 m= 63 mr = 735 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 216 time to turn everything in is 0.4600000 number of dielectric boundary points 28075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 339 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23468 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) : 0.5226839 object centre at (A) : 54.55400 20.20500 49.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2369666E-03 9.9618770E-03 midg,1,midg; midg,igrid,midg 5.7274420E-03 5.7277293E-03 1,midg,midg; igrid,midg,midg 8.1135012E-04 7.2590802E-03 gauss-seidel spectral radius is 0.9980626 estimated iterations to convergence 181 setup time was (sec) 0.7400000 now iterating at: 08:14:52 rms-change max change #iterations 3.177410 158.8757 at 10iterations 1.286115 48.40045 at 20iterations 0.5193605 20.97148 at 30iterations 0.2117530 7.489849 at 40iterations 8.5695505E-02 3.181904 at 50iterations 3.4759879E-02 1.339887 at 60iterations 1.4077721E-02 0.5117874 at 70iterations 5.7358448E-03 0.2211618 at 80iterations 2.3326336E-03 8.4238052E-02 at 90iterations 9.4923744E-04 3.3689022E-02 at 100iterations 3.8778887E-04 1.5358210E-02 at 110iterations 1.5921485E-04 5.8746338E-03 at 120iterations finished qdiffx linear iterations at : 08:14:58 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.5921485E-04 5.8746338E-03 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 08:14:59 7.465u 0.252s 0:08.06 95.6% 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 08:14:59 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 !!! WARNING: NAP 528 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.352077 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): 20.49900 88.60900 ymin,ymax (A): -7.435000 47.84500 zmin,zma (A): 23.44400 76.17700 x,y,z range (A): 68.11000 55.28000 52.73300 scale (grids/A): 2.352077 object centre (A): 54.55400 20.20500 49.81050 number of atom coordinates read : 3277 total number of charged atoms : 3091 net assigned charge : 9.500010 assigned positive charge : 482.4337 centred at (gu) : 84.22425 92.96901 88.94077 assigned negative charge : -472.9351 centred at (gu) : 83.90762 93.00131 88.82304 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 151658 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29095 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 66761 mr = 108857 m= 17083 mr = 52149 m= 2470 mr = 12316 m= 178 mr = 1492 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 634 time to turn everything in is 1.090000 number of dielectric boundary points 63264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 24685 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) : 1.568052 object centre at (A) : 54.55400 20.20500 49.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1469390E-02 0.1804176 midg,1,midg; midg,igrid,midg 9.1239430E-02 8.1299983E-02 1,midg,midg; igrid,midg,midg -0.1206644 0.1186072 gauss-seidel spectral radius is 0.9991084 estimated iterations to convergence 265 setup time was (sec) 1.400000 now iterating at: 08:15:01 rms-change max change #iterations 8.379632 251.6304 at 10iterations 4.688407 122.1495 at 20iterations 2.604435 70.33066 at 30iterations 1.439768 36.35640 at 40iterations 0.7912608 18.45740 at 50iterations 0.4354919 9.569503 at 60iterations 0.2385552 5.774622 at 70iterations 0.1304769 3.467644 at 80iterations 7.1419738E-02 1.639297 at 90iterations 3.8983248E-02 0.8830986 at 100iterations 2.1217396E-02 0.4590607 at 110iterations 1.1616820E-02 0.2521443 at 120iterations 6.3267481E-03 0.1407318 at 130iterations 3.4420597E-03 7.0128918E-02 at 140iterations 1.8721888E-03 3.9561868E-02 at 150iterations 1.0191522E-03 2.1640778E-02 at 160iterations 5.5689935E-04 1.1554241E-02 at 170iterations 3.0291098E-04 6.8588257E-03 at 180iterations finished qdiffx linear iterations at : 08:15:13 total time elapsed so far: 13.53000 # loops : 180 mean,max change (kT/e) : 3.0291098E-04 6.8588257E-03 energy calculations done at 13.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 08:15:13 13.700u 0.249s 0:14.36 97.0% 0+0k 0+0io 0pf+0w