Thu Jan 19 13:31:57 PST 2012 #!/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 Thu Jan 19 2012 at 13:31:57 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6791 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 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: 0.4230692 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): 15.71900 99.86600 ymin,ymax (A): -3.360000 63.74200 zmin,zma (A): 144.4910 222.6570 x,y,z range (A): 84.14700 67.10200 78.16600 scale (grids/A): 0.4230692 object centre (A): 57.79250 30.19100 183.5740 number of atom coordinates read : 6791 total number of charged atoms : 6620 net assigned charge : 1.200030 assigned positive charge : 1029.728 centred at (gu) : 91.51233 89.78212 90.37747 assigned negative charge : -1028.538 centred at (gu) : 91.50178 89.78548 90.31508 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7118 nv = 96 ne = 84 npr = 135845 no. pairs analyzed = 135845 no. exposed pairs = 8770 no. arc points = 60497 no. surface atoms = 2950 nbur = 3841 mkacc time = 0.2300000 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 = 1.988000 m= 195 mr = 3338 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4899 ## 1065 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1581116E-12 2.9948880E-12 midg,1,midg; midg,igrid,midg 2.9255320E-13 -1.5226742E-16 1,midg,midg; igrid,midg,midg -1.8112890E-13 9.1560180E-13 gauss-seidel spectral radius is 0.9716612 estimated iterations to convergence 50 setup time was (sec) 0.6200000 now iterating at: 13:31:59 rms-change max change #iterations 2.7888158E-02 4.719584 at 10iterations 1.8604741E-03 0.3381920 at 20iterations 6.0032331E-04 0.1175232 at 30iterations 2.1613245E-04 4.1574478E-02 at 40iterations 7.7698111E-05 1.4717102E-02 at 50iterations finished qdiffx linear iterations at : 13:32:03 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 7.7698111E-05 1.4717102E-02 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 13:32:04 3.775u 0.189s 0:06.68 59.1% 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 Thu Jan 19 2012 at 13:32:04 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6791 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 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: 1.269207 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): 15.71900 99.86600 ymin,ymax (A): -3.360000 63.74200 zmin,zma (A): 144.4910 222.6570 x,y,z range (A): 84.14700 67.10200 78.16600 scale (grids/A): 1.269207 object centre (A): 57.79250 30.19100 183.5740 number of atom coordinates read : 6791 total number of charged atoms : 6620 net assigned charge : 1.200030 assigned positive charge : 1029.728 centred at (gu) : 94.53531 89.34438 91.13052 assigned negative charge : -1028.538 centred at (gu) : 94.50504 89.35625 90.94441 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 84267 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60497 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 19110 mr = 55372 m= 874 mr = 11228 m= 11 mr = 179 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 377 time to turn everything in is 0.4500000 number of dielectric boundary points 37484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1172 ## 53 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 45439 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) : 0.4230692 object centre at (A) : 57.79250 30.19100 183.5740 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6041273E-03 2.0541169E-03 midg,1,midg; midg,igrid,midg 1.4113837E-04 8.5944671E-04 1,midg,midg; igrid,midg,midg -1.2306675E-03 -1.3632352E-03 gauss-seidel spectral radius is 0.9973063 estimated iterations to convergence 154 setup time was (sec) 0.6800000 now iterating at: 13:32:05 rms-change max change #iterations 2.937224 135.4662 at 10iterations 1.013521 39.01997 at 20iterations 0.3486432 13.02009 at 30iterations 0.1201208 4.108847 at 40iterations 4.1839279E-02 1.478120 at 50iterations 1.4562818E-02 0.5086856 at 60iterations 5.1431912E-03 0.1693277 at 70iterations 1.9337476E-03 6.8408966E-02 at 80iterations 8.3810155E-04 3.3533096E-02 at 90iterations 4.4740306E-04 1.8716812E-02 at 100iterations 2.7883460E-04 1.0486603E-02 at 110iterations 1.8483968E-04 6.6452026E-03 at 120iterations finished qdiffx linear iterations at : 13:32:19 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.8483968E-04 6.6452026E-03 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 13:32:20 7.901u 0.190s 0:15.91 50.8% 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 Thu Jan 19 2012 at 13:32:20 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6791 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 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: 1.903811 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): 15.71900 99.86600 ymin,ymax (A): -3.360000 63.74200 zmin,zma (A): 144.4910 222.6570 x,y,z range (A): 84.14700 67.10200 78.16600 scale (grids/A): 1.903811 object centre (A): 57.79250 30.19100 183.5740 number of atom coordinates read : 6791 total number of charged atoms : 6620 net assigned charge : 1.200030 assigned positive charge : 1029.728 centred at (gu) : 96.80236 89.01598 91.69527 assigned negative charge : -1028.538 centred at (gu) : 96.75761 89.03427 91.41664 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 198305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60497 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 74714 mr = 139113 m= 12630 mr = 54731 m= 802 mr = 7714 m= 7 mr = 278 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1279 time to turn everything in is 1.000000 number of dielectric boundary points 84622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 52106 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) : 1.269207 object centre at (A) : 57.79250 30.19100 183.5740 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2396614 3.8529854E-02 midg,1,midg; midg,igrid,midg 1.2781442E-02 1.4957826E-02 1,midg,midg; igrid,midg,midg 2.3778852E-02 3.3519384E-02 gauss-seidel spectral radius is 0.9989474 estimated iterations to convergence 244 setup time was (sec) 1.250000 now iterating at: 13:32:21 rms-change max change #iterations 9.069458 293.0850 at 10iterations 4.861014 124.6828 at 20iterations 2.570997 68.84052 at 30iterations 1.357849 32.01712 at 40iterations 0.7125300 16.81518 at 50iterations 0.3724055 9.143776 at 60iterations 0.1948899 4.523695 at 70iterations 0.1013459 2.640167 at 80iterations 5.2645706E-02 1.217163 at 90iterations 2.7323831E-02 0.6147537 at 100iterations 1.4178652E-02 0.3167572 at 110iterations 7.3559815E-03 0.1542463 at 120iterations 3.8225015E-03 8.7161064E-02 at 130iterations 1.9861644E-03 3.8909912E-02 at 140iterations 1.0368632E-03 2.5943756E-02 at 150iterations 5.4619665E-04 1.1109352E-02 at 160iterations 2.9276448E-04 6.4716339E-03 at 170iterations 1.6145338E-04 3.4847260E-03 at 180iterations finished qdiffx linear iterations at : 13:32:44 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 1.6145338E-04 3.4847260E-03 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 13:32:45 13.573u 0.219s 0:25.20 54.6% 0+0k 0+0io 0pf+0w