Sat Oct 15 14:15:33 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 15 2011 at 14:15:33 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: 278 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 : 675.7327 centred at (gu) : 91.33620 89.12103 87.24285 assigned negative charge : -671.4365 centred at (gu) : 91.45785 89.23307 87.14960 start vw surface at 0.2200000 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 = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 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 0.6700000 number of grid points assigned charge 10413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7475630E-10 2.5301261E-10 midg,1,midg; midg,igrid,midg 7.3817208E-10 -2.8036390E-10 1,midg,midg; igrid,midg,midg 4.4421400E-10 -5.6436789E-10 gauss-seidel spectral radius is 0.9813575 estimated iterations to convergence 60 setup time was (sec) 0.8200000 now iterating at: 14:15:34 rms-change max change #iterations 7.4040450E-02 9.491081 at 10iterations 4.9085375E-03 0.7609024 at 20iterations 9.4323803E-04 0.1450958 at 30iterations 4.0178356E-04 6.5155029E-02 at 40iterations 1.8210156E-04 3.0192375E-02 at 50iterations finished qdiffx linear iterations at : 14:15:37 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 1.8210156E-04 3.0192375E-02 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 14:15:38 4.415u 0.268s 0:05.01 93.2% 0+0k 0+0io 6pf+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 14:15:38 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: 278 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 : 675.7327 centred at (gu) : 94.00748 87.36153 81.72675 assigned negative charge : -671.4365 centred at (gu) : 94.37302 87.69881 81.44820 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 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 = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 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 0.9600000 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 6.5244758E-03 1.0040324E-02 midg,1,midg; midg,igrid,midg 4.5651039E-03 -1.3272692E-02 1,midg,midg; igrid,midg,midg 1.3760221E-02 -1.8529325E-03 gauss-seidel spectral radius is 0.9981981 estimated iterations to convergence 187 setup time was (sec) 1.140000 now iterating at: 14:15:39 rms-change max change #iterations 3.887747 167.2208 at 10iterations 1.628202 54.88701 at 20iterations 0.6784500 21.75636 at 30iterations 0.2860041 9.182196 at 40iterations 0.1194983 3.861502 at 50iterations 5.0143156E-02 1.582364 at 60iterations 2.1124288E-02 0.7650423 at 70iterations 8.9852493E-03 0.2907867 at 80iterations 3.9093252E-03 0.1285019 at 90iterations 1.8112805E-03 6.6705704E-02 at 100iterations 9.5259387E-04 3.5569191E-02 at 110iterations 5.9293443E-04 2.1057367E-02 at 120iterations finished qdiffx linear iterations at : 14:15:48 total time elapsed so far: 9.930000 # loops : 120 mean,max change (kT/e) : 5.9293443E-04 2.1057367E-02 energy calculations done at 9.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 14:15:48 10.121u 0.313s 0:10.72 97.2% 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 14:15:48 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: 278 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 : 675.7327 centred at (gu) : 96.01102 86.04205 77.58978 assigned negative charge : -671.4365 centred at (gu) : 96.55952 86.54843 77.17223 start vw surface at 0.2000000 fill in re-entrant regions at 0.6300000 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 = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.970000 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 2.140000 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 0.6027960 0.2295692 midg,1,midg; midg,igrid,midg 3.9140385E-02 -0.2732401 1,midg,midg; igrid,midg,midg 0.2280067 -6.1769257E-03 gauss-seidel spectral radius is 0.9991850 estimated iterations to convergence 277 setup time was (sec) 2.330000 now iterating at: 14:15:51 rms-change max change #iterations 10.34353 291.1338 at 10iterations 5.973624 130.4033 at 20iterations 3.427762 77.92595 at 30iterations 1.954669 42.36993 at 40iterations 1.107997 21.61084 at 50iterations 0.6264810 14.48172 at 60iterations 0.3537198 6.821421 at 70iterations 0.1998174 4.182446 at 80iterations 0.1125573 2.261473 at 90iterations 6.3183993E-02 1.214154 at 100iterations 3.5527658E-02 0.6830568 at 110iterations 1.9956131E-02 0.4084778 at 120iterations 1.1205759E-02 0.2149811 at 130iterations 6.2812981E-03 0.1434746 at 140iterations 3.5272983E-03 7.5415611E-02 at 150iterations 1.9791061E-03 3.5938263E-02 at 160iterations 1.1172235E-03 2.1987915E-02 at 170iterations 6.3348538E-04 1.1573792E-02 at 180iterations finished qdiffx linear iterations at : 14:16:06 total time elapsed so far: 17.21000 # loops : 180 mean,max change (kT/e) : 6.3348538E-04 1.1573792E-02 energy calculations done at 17.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.40000 DelPhi exited at 14:16:07 17.398u 0.370s 0:18.08 98.2% 0+0k 0+0io 0pf+0w