Sat Oct 8 22:40:59 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 Sat Oct 8 2011 at 22:40:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: MG6 609 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5885757 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): 82.00800 125.5820 ymin,ymax (A): 61.01500 121.5000 zmin,zma (A): 54.83800 109.7280 x,y,z range (A): 43.57400 60.48500 54.89000 scale (grids/A): 0.5885757 object centre (A): 103.7950 91.25750 82.28300 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 11.90002 assigned positive charge : 380.2529 centred at (gu) : 90.04939 89.77430 89.35587 assigned negative charge : -368.3538 centred at (gu) : 90.00409 89.74603 89.40974 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6043 nv = 96 ne = 84 npr = 51898 no. pairs analyzed = 51898 no. exposed pairs = 3346 no. arc points = 23447 no. surface atoms = 1131 nbur = 1460 mkacc time = 0.1500000 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 = 1.484000 m= 296 mr = 3148 m= 1 mr = 21 m= 0 mr = 0 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 3171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2449 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7578 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5287810E-09 1.8912027E-09 midg,1,midg; midg,igrid,midg 2.9401168E-09 3.9562855E-09 1,midg,midg; igrid,midg,midg 2.3565823E-09 4.6218651E-09 gauss-seidel spectral radius is 0.9850706 estimated iterations to convergence 67 setup time was (sec) 0.6200000 now iterating at: 22:41:00 rms-change max change #iterations 9.5254727E-02 15.18860 at 10iterations 8.6258911E-03 1.390293 at 20iterations 1.2792412E-03 0.2420387 at 30iterations 3.5036015E-04 7.3516846E-02 at 40iterations 1.1021401E-04 2.3014069E-02 at 50iterations finished qdiffx linear iterations at : 22:41:03 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.1021401E-04 2.3014069E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 22:41:04 4.073u 0.259s 0:04.59 94.1% 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 Sat Oct 8 2011 at 22:41:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: MG6 609 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.765727 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): 82.00800 125.5820 ymin,ymax (A): 61.01500 121.5000 zmin,zma (A): 54.83800 109.7280 x,y,z range (A): 43.57400 60.48500 54.89000 scale (grids/A): 1.765727 object centre (A): 103.7950 91.25750 82.28300 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 11.90002 assigned positive charge : 380.2529 centred at (gu) : 90.14737 89.32241 88.06732 assigned negative charge : -368.3538 centred at (gu) : 90.01218 89.23796 88.22930 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 65633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23447 grid for indexing accessible points = 1.400000 m= 22422 mr = 44272 m= 2883 mr = 15875 m= 121 mr = 1604 m= 0 mr = 24 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 29284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 210 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19080 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) : 0.5885757 object centre at (A) : 103.7950 91.25750 82.28300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9742420E-02 8.0911499E-03 midg,1,midg; midg,igrid,midg 3.4479661E-05 3.8813658E-02 1,midg,midg; igrid,midg,midg 6.7725065E-03 1.7471710E-02 gauss-seidel spectral radius is 0.9984236 estimated iterations to convergence 200 setup time was (sec) 0.9000000 now iterating at: 22:41:05 rms-change max change #iterations 3.541754 186.4607 at 10iterations 1.558019 56.24960 at 20iterations 0.6860135 25.45932 at 30iterations 0.3044054 12.75291 at 40iterations 0.1352665 4.969561 at 50iterations 5.9781350E-02 1.902055 at 60iterations 2.6653480E-02 0.9296618 at 70iterations 1.1981450E-02 0.4171906 at 80iterations 5.4882485E-03 0.2031059 at 90iterations 2.6359120E-03 0.1071587 at 100iterations 1.3394014E-03 5.6753159E-02 at 110iterations 7.4980455E-04 3.1682968E-02 at 120iterations finished qdiffx linear iterations at : 22:41:13 total time elapsed so far: 9.140000 # loops : 120 mean,max change (kT/e) : 7.4980455E-04 3.1682968E-02 energy calculations done at 9.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 22:41:14 9.325u 0.289s 0:09.92 96.7% 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 Sat Oct 8 2011 at 22:41:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: MG6 609 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.648591 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): 82.00800 125.5820 ymin,ymax (A): 61.01500 121.5000 zmin,zma (A): 54.83800 109.7280 x,y,z range (A): 43.57400 60.48500 54.89000 scale (grids/A): 2.648591 object centre (A): 103.7950 91.25750 82.28300 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 11.90002 assigned positive charge : 380.2529 centred at (gu) : 90.22092 88.98337 87.10075 assigned negative charge : -368.3538 centred at (gu) : 90.01833 88.85690 87.34396 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 151848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23447 grid for indexing accessible points = 1.400000 m= 74218 mr = 107977 m= 24610 mr = 59271 m= 4884 mr = 19044 m= 546 mr = 3478 m= 11 mr = 325 m= 0 mr = 7 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 66015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 19628 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) : 1.765727 object centre at (A) : 103.7950 91.25750 82.28300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3683580 3.0107753E-02 midg,1,midg; midg,igrid,midg -1.5169388E-02 0.6523722 1,midg,midg; igrid,midg,midg 6.7593493E-02 0.2179371 gauss-seidel spectral radius is 0.9992064 estimated iterations to convergence 280 setup time was (sec) 1.820000 now iterating at: 22:41:16 rms-change max change #iterations 8.819416 319.6306 at 10iterations 5.105356 136.1109 at 20iterations 2.943508 66.74479 at 30iterations 1.681200 39.06324 at 40iterations 0.9580448 26.08236 at 50iterations 0.5451858 12.73969 at 60iterations 0.3097249 7.085343 at 70iterations 0.1757243 4.023962 at 80iterations 9.9633090E-02 2.013446 at 90iterations 5.6134921E-02 1.197178 at 100iterations 3.1842604E-02 0.6766205 at 110iterations 1.8127874E-02 0.3744221 at 120iterations 1.0303617E-02 0.2156029 at 130iterations 5.9205964E-03 0.1351790 at 140iterations 3.4533623E-03 8.0131531E-02 at 150iterations 2.0754072E-03 5.5824280E-02 at 160iterations 1.2952526E-03 3.1204224E-02 at 170iterations 8.5893896E-04 2.2251129E-02 at 180iterations finished qdiffx linear iterations at : 22:41:29 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 8.5893896E-04 2.2251129E-02 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.47000 DelPhi exited at 22:41:30 15.476u 0.310s 0:16.05 98.3% 0+0k 0+0io 0pf+0w