Mon Oct 10 14:00:48 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 14:00:48 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4452 !!! WARNING: HEM 915 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5097146 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): 2.988000 61.92700 ymin,ymax (A): -50.09100 16.64900 zmin,zma (A): -16.17900 53.66400 x,y,z range (A): 58.93900 66.74000 69.84300 scale (grids/A): 0.5097146 object centre (A): 32.45750 -16.72100 18.74250 number of atom coordinates read : 4452 total number of charged atoms : 4220 net assigned charge : 7.300029 assigned positive charge : 649.1339 centred at (gu) : 90.03095 88.58193 93.92638 assigned negative charge : -641.8376 centred at (gu) : 89.96789 88.46250 93.96995 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7444 nv = 96 ne = 84 npr = 89287 no. pairs analyzed = 89287 no. exposed pairs = 5834 no. arc points = 41572 no. surface atoms = 1969 nbur = 2483 mkacc time = 0.2600000 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 = 1.680000 m= 280 mr = 3614 m= 0 mr = 4 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3983 ## 565 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 9842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3313272E-11 1.5628658E-11 midg,1,midg; midg,igrid,midg -2.3670008E-10 2.5008992E-10 1,midg,midg; igrid,midg,midg -3.3037399E-11 2.4446620E-10 gauss-seidel spectral radius is 0.9803085 estimated iterations to convergence 59 setup time was (sec) 0.8000000 now iterating at: 14:00:49 rms-change max change #iterations 6.4679138E-02 11.03525 at 10iterations 4.2575053E-03 0.6606674 at 20iterations 6.0081814E-04 7.2299957E-02 at 30iterations 1.3441256E-04 1.3847351E-02 at 40iterations 3.1592343E-05 3.2950938E-03 at 50iterations finished qdiffx linear iterations at : 14:00:52 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 3.1592343E-05 3.2950938E-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) 4.280000 DelPhi exited at 14:00:53 4.287u 0.260s 0:05.14 88.3% 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 14:00:53 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4452 !!! WARNING: HEM 915 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.529144 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): 2.988000 61.92700 ymin,ymax (A): -50.09100 16.64900 zmin,zma (A): -16.17900 53.66400 x,y,z range (A): 58.93900 66.74000 69.84300 scale (grids/A): 1.529144 object centre (A): 32.45750 -16.72100 18.74250 number of atom coordinates read : 4452 total number of charged atoms : 4220 net assigned charge : 7.300029 assigned positive charge : 649.1339 centred at (gu) : 90.09152 85.74461 101.7776 assigned negative charge : -641.8376 centred at (gu) : 89.90314 85.38698 101.9094 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 83608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41572 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23929 mr = 54853 m= 2283 mr = 15835 m= 45 mr = 986 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 38191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 451 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 31721 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) : 0.5097146 object centre at (A) : 32.45750 -16.72100 18.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7742461E-02 2.6988581E-02 midg,1,midg; midg,igrid,midg -1.8584382E-02 7.7528004E-03 1,midg,midg; igrid,midg,midg -9.3815261E-03 1.1127386E-02 gauss-seidel spectral radius is 0.9980820 estimated iterations to convergence 181 setup time was (sec) 1.070000 now iterating at: 14:00:54 rms-change max change #iterations 3.595077 154.3055 at 10iterations 1.457098 55.04931 at 20iterations 0.5905296 19.01452 at 30iterations 0.2404395 8.001999 at 40iterations 9.8157883E-02 3.653491 at 50iterations 3.9952844E-02 1.396442 at 60iterations 1.6328111E-02 0.5739708 at 70iterations 6.7599164E-03 0.2254980 at 80iterations 2.7891360E-03 9.4924927E-02 at 90iterations 1.1638055E-03 3.7837982E-02 at 100iterations 5.0404604E-04 1.5726089E-02 at 110iterations 2.2861396E-04 7.7610016E-03 at 120iterations finished qdiffx linear iterations at : 14:01:03 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 2.2861396E-04 7.7610016E-03 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 14:01:04 9.639u 0.283s 0:10.68 92.7% 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 Mon Oct 10 2011 at 14:01:04 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4452 !!! WARNING: HEM 915 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.293716 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): 2.988000 61.92700 ymin,ymax (A): -50.09100 16.64900 zmin,zma (A): -16.17900 53.66400 x,y,z range (A): 58.93900 66.74000 69.84300 scale (grids/A): 2.293716 object centre (A): 32.45750 -16.72100 18.74250 number of atom coordinates read : 4452 total number of charged atoms : 4220 net assigned charge : 7.300029 assigned positive charge : 649.1339 centred at (gu) : 90.13675 83.61640 107.6660 assigned negative charge : -641.8376 centred at (gu) : 89.85466 83.08041 107.8639 start vw surface at 0.2200000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 194680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41572 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 84428 mr = 135643 m= 22722 mr = 64970 m= 3247 mr = 16335 m= 158 mr = 1985 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 86249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 33672 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) : 1.529144 object centre at (A) : 32.45750 -16.72100 18.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3976288 0.6595331 midg,1,midg; midg,igrid,midg -0.3255772 5.1582314E-02 1,midg,midg; igrid,midg,midg -0.1615044 0.1961199 gauss-seidel spectral radius is 0.9991474 estimated iterations to convergence 271 setup time was (sec) 2.180000 now iterating at: 14:01:06 rms-change max change #iterations 9.760572 260.1590 at 10iterations 5.586784 121.9388 at 20iterations 3.163343 69.05239 at 30iterations 1.777258 35.65702 at 40iterations 0.9972378 20.71185 at 50iterations 0.5568034 10.99205 at 60iterations 0.3103222 6.410391 at 70iterations 0.1721442 3.294735 at 80iterations 9.5712475E-02 2.210522 at 90iterations 5.3157344E-02 1.023327 at 100iterations 2.9364960E-02 0.6309638 at 110iterations 1.6283359E-02 0.3129463 at 120iterations 9.0224193E-03 0.1868248 at 130iterations 4.9926140E-03 9.7885132E-02 at 140iterations 2.7577605E-03 5.1166534E-02 at 150iterations 1.5314713E-03 2.8317451E-02 at 160iterations 8.5073343E-04 1.7192841E-02 at 170iterations 4.7271207E-04 9.1085434E-03 at 180iterations finished qdiffx linear iterations at : 14:01:20 total time elapsed so far: 16.20000 # loops : 180 mean,max change (kT/e) : 4.7271207E-04 9.1085434E-03 energy calculations done at 16.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.38000 DelPhi exited at 14:01:21 16.383u 0.301s 0:17.57 94.9% 0+0k 0+0io 0pf+0w