Sat Oct 15 14:16:07 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 15 2011 at 14:16:07 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4498 !!! WARNING: HEM 808 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: 0.5239840 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): -24.34300 39.95100 ymin,ymax (A): -17.98800 44.85600 zmin,zma (A): 7.097000 75.03800 x,y,z range (A): 64.29400 62.84400 67.94100 scale (grids/A): 0.5239840 object centre (A): 7.804000 13.43400 41.06750 number of atom coordinates read : 4498 total number of charged atoms : 4259 net assigned charge : 4.300026 assigned positive charge : 677.7330 centred at (gu) : 91.32965 89.12203 87.23341 assigned negative charge : -673.4365 centred at (gu) : 91.44935 89.23523 87.14235 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7944 nv = 96 ne = 84 npr = 89374 no. pairs analyzed = 89374 no. exposed pairs = 6047 no. arc points = 41569 no. surface atoms = 2005 nbur = 2493 mkacc time = 0.2500000 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= 318 mr = 3943 m= 0 mr = 6 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4021 ## 539 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 10413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5989746E-10 2.4836466E-10 midg,1,midg; midg,igrid,midg 7.4510198E-10 -2.8587188E-10 1,midg,midg; igrid,midg,midg 4.4007026E-10 -5.5408772E-10 gauss-seidel spectral radius is 0.9813575 estimated iterations to convergence 60 setup time was (sec) 0.8000000 now iterating at: 14:16:08 rms-change max change #iterations 7.4874759E-02 9.533008 at 10iterations 4.9649524E-03 0.7736740 at 20iterations 9.4360026E-04 0.1416435 at 30iterations 3.9918764E-04 6.4256668E-02 at 40iterations 1.8062412E-04 2.9861450E-02 at 50iterations finished qdiffx linear iterations at : 14:16:11 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 1.8062412E-04 2.9861450E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 14:16:12 4.406u 0.288s 0:05.02 93.2% 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 15 2011 at 14:16:12 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4498 !!! WARNING: HEM 808 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: 1.571952 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): -24.34300 39.95100 ymin,ymax (A): -17.98800 44.85600 zmin,zma (A): 7.097000 75.03800 x,y,z range (A): 64.29400 62.84400 67.94100 scale (grids/A): 1.571952 object centre (A): 7.804000 13.43400 41.06750 number of atom coordinates read : 4498 total number of charged atoms : 4259 net assigned charge : 4.300026 assigned positive charge : 677.7330 centred at (gu) : 93.98788 87.36464 81.69849 assigned negative charge : -673.4365 centred at (gu) : 94.34751 87.70529 81.42639 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 89533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41569 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 26789 mr = 60136 m= 2531 mr = 17570 m= 74 mr = 1016 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 40204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 470 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 32229 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) : 0.5239840 object centre at (A) : 7.804000 13.43400 41.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3960000E-03 1.0011524E-02 midg,1,midg; midg,igrid,midg 4.6648537E-03 -1.3353950E-02 1,midg,midg; igrid,midg,midg 1.3509325E-02 -1.8115913E-03 gauss-seidel spectral radius is 0.9981981 estimated iterations to convergence 187 setup time was (sec) 1.120000 now iterating at: 14:16:13 rms-change max change #iterations 3.908058 167.2208 at 10iterations 1.636448 54.88700 at 20iterations 0.6820349 22.06536 at 30iterations 0.2875895 8.972581 at 40iterations 0.1201829 3.896426 at 50iterations 5.0421707E-02 1.609360 at 60iterations 2.1246755E-02 0.7629189 at 70iterations 9.0446677E-03 0.3044147 at 80iterations 3.9344062E-03 0.1292095 at 90iterations 1.8248659E-03 6.4804077E-02 at 100iterations 9.6110674E-04 3.5798788E-02 at 110iterations 5.9875997E-04 2.1176875E-02 at 120iterations finished qdiffx linear iterations at : 14:16:22 total time elapsed so far: 9.890000 # loops : 120 mean,max change (kT/e) : 5.9875997E-04 2.1176875E-02 energy calculations done at 9.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.08000 DelPhi exited at 14:16:23 10.081u 0.332s 0:10.71 97.1% 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 15 2011 at 14:16:23 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4498 !!! WARNING: HEM 808 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: 2.357928 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): -24.34300 39.95100 ymin,ymax (A): -17.98800 44.85600 zmin,zma (A): 7.097000 75.03800 x,y,z range (A): 64.29400 62.84400 67.94100 scale (grids/A): 2.357928 object centre (A): 7.804000 13.43400 41.06750 number of atom coordinates read : 4498 total number of charged atoms : 4259 net assigned charge : 4.300026 assigned positive charge : 677.7330 centred at (gu) : 95.98166 86.04672 77.54743 assigned negative charge : -673.4365 centred at (gu) : 96.52125 86.55814 77.13951 start vw surface at 0.2100000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 208048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41569 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 94296 mr = 147618 m= 24939 mr = 72969 m= 3603 mr = 17561 m= 209 mr = 2036 m= 5 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 90845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 34006 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) : 1.571952 object centre at (A) : 7.804000 13.43400 41.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6184688 0.2291403 midg,1,midg; midg,igrid,midg 4.0501151E-02 -0.2747347 1,midg,midg; igrid,midg,midg 0.2240158 -5.8218869E-03 gauss-seidel spectral radius is 0.9991850 estimated iterations to convergence 277 setup time was (sec) 2.330000 now iterating at: 14:16:25 rms-change max change #iterations 10.38210 291.1337 at 10iterations 5.994957 130.3938 at 20iterations 3.439204 77.87177 at 30iterations 1.960917 42.36270 at 40iterations 1.111400 22.11695 at 50iterations 0.6283748 14.54447 at 60iterations 0.3547257 6.807278 at 70iterations 0.2003658 4.211872 at 80iterations 0.1128778 2.266250 at 90iterations 6.3359372E-02 1.217404 at 100iterations 3.5626072E-02 0.6895790 at 110iterations 2.0010209E-02 0.4085159 at 120iterations 1.1237385E-02 0.2155151 at 130iterations 6.2990799E-03 0.1444740 at 140iterations 3.5378735E-03 7.5683594E-02 at 150iterations 1.9858782E-03 3.5633087E-02 at 160iterations 1.1220726E-03 2.2109985E-02 at 170iterations 6.3714839E-04 1.1756897E-02 at 180iterations finished qdiffx linear iterations at : 14:16:40 total time elapsed so far: 17.24000 # loops : 180 mean,max change (kT/e) : 6.3714839E-04 1.1756897E-02 energy calculations done at 17.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.43000 DelPhi exited at 14:16:41 17.432u 0.359s 0:18.21 97.6% 0+0k 0+0io 0pf+0w