Sat Oct 15 13:53:12 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 13:53:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5683995 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): -14.52400 39.93600 ymin,ymax (A): -22.08900 23.09300 zmin,zma (A): -17.07900 45.55300 x,y,z range (A): 54.46000 45.18200 62.63200 scale (grids/A): 0.5683995 object centre (A): 12.70600 0.5019999 14.23700 number of atom coordinates read : 2972 total number of charged atoms : 2830 net assigned charge : 0.5000303 assigned positive charge : 443.4043 centred at (gu) : 90.05613 89.31161 89.96640 assigned negative charge : -442.9053 centred at (gu) : 90.03468 89.43040 90.02293 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6342 nv = 96 ne = 84 npr = 59409 no. pairs analyzed = 59409 no. exposed pairs = 3764 no. arc points = 27155 no. surface atoms = 1274 nbur = 1698 mkacc time = 0.1000000 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 = 1.512000 m= 273 mr = 3302 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2100000 number of dielectric boundary points 3294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2713 ## 283 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8075 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9910779E-10 -7.7777051E-10 midg,1,midg; midg,igrid,midg 2.1227349E-09 -1.4614910E-09 1,midg,midg; igrid,midg,midg -2.5560590E-10 3.8181497E-10 gauss-seidel spectral radius is 0.9840334 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 13:53:13 rms-change max change #iterations 8.9495584E-02 13.91185 at 10iterations 6.5641897E-03 1.091277 at 20iterations 4.9034128E-04 8.5459709E-02 at 30iterations 3.7234495E-05 5.6915283E-03 at 40iterations 2.9590653E-06 5.0735474E-04 at 50iterations finished qdiffx linear iterations at : 13:53:16 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 2.9590653E-06 5.0735474E-04 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 13:53:17 3.734u 0.224s 0:04.27 92.5% 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 13:53:17 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 = 2972 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.705199 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): -14.52400 39.93600 ymin,ymax (A): -22.08900 23.09300 zmin,zma (A): -17.07900 45.55300 x,y,z range (A): 54.46000 45.18200 62.63200 scale (grids/A): 1.705199 object centre (A): 12.70600 0.5019999 14.23700 number of atom coordinates read : 2972 total number of charged atoms : 2830 net assigned charge : 0.5000303 assigned positive charge : 443.4043 centred at (gu) : 90.16811 87.93423 89.89836 assigned negative charge : -442.9053 centred at (gu) : 90.10369 88.29086 90.06876 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27155 grid for indexing accessible points = 1.400000 m= 22373 mr = 46537 m= 2674 mr = 15729 m= 78 mr = 1347 m= 0 mr = 18 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 955 time to turn everything in is 0.3500000 number of dielectric boundary points 30680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21884 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) : 0.5683995 object centre at (A) : 12.70600 0.5019999 14.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8642763E-03 -1.6131960E-02 midg,1,midg; midg,igrid,midg 1.2692434E-02 -6.6948663E-03 1,midg,midg; igrid,midg,midg 3.8790444E-03 1.1291590E-03 gauss-seidel spectral radius is 0.9983463 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 13:53:17 rms-change max change #iterations 3.651905 171.1299 at 10iterations 1.575077 61.60463 at 20iterations 0.6821386 23.80287 at 30iterations 0.2961071 10.50123 at 40iterations 0.1286308 4.382618 at 50iterations 5.5836242E-02 2.007837 at 60iterations 2.4214730E-02 0.8717316 at 70iterations 1.0486109E-02 0.3695142 at 80iterations 4.5613428E-03 0.1532550 at 90iterations 1.9940000E-03 6.5550804E-02 at 100iterations 8.6436444E-04 2.9438019E-02 at 110iterations 3.7875285E-04 1.2654305E-02 at 120iterations finished qdiffx linear iterations at : 13:53:25 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 3.7875285E-04 1.2654305E-02 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 13:53:26 8.601u 0.274s 0:09.21 96.3% 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 Sat Oct 15 2011 at 13:53:26 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 = 2972 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.557798 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): -14.52400 39.93600 ymin,ymax (A): -22.08900 23.09300 zmin,zma (A): -17.07900 45.55300 x,y,z range (A): 54.46000 45.18200 62.63200 scale (grids/A): 2.557798 object centre (A): 12.70600 0.5019999 14.23700 number of atom coordinates read : 2972 total number of charged atoms : 2830 net assigned charge : 0.5000303 assigned positive charge : 443.4043 centred at (gu) : 90.25188 86.90117 89.84742 assigned negative charge : -442.9053 centred at (gu) : 90.15540 87.43610 90.10292 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 160371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27155 grid for indexing accessible points = 1.400000 m= 75547 mr = 113835 m= 23858 mr = 59992 m= 4217 mr = 18290 m= 372 mr = 2870 m= 5 mr = 193 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 3323 time to turn everything in is 0.8400000 number of dielectric boundary points 69190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 22624 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) : 1.705199 object centre at (A) : 12.70600 0.5019999 14.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1982269 -0.2239174 midg,1,midg; midg,igrid,midg 0.1390714 -8.0920495E-02 1,midg,midg; igrid,midg,midg 3.3145875E-02 0.1204005 gauss-seidel spectral radius is 0.9991895 estimated iterations to convergence 277 setup time was (sec) 1.110000 now iterating at: 13:53:27 rms-change max change #iterations 9.163012 311.7963 at 10iterations 5.188947 120.2615 at 20iterations 2.921769 72.56232 at 30iterations 1.647596 34.15163 at 40iterations 0.9271841 20.03093 at 50iterations 0.5195692 10.65694 at 60iterations 0.2909992 5.934266 at 70iterations 0.1628506 3.481695 at 80iterations 9.1444597E-02 1.812077 at 90iterations 5.1183730E-02 0.9724145 at 100iterations 2.8645651E-02 0.5676575 at 110iterations 1.5982302E-02 0.3156395 at 120iterations 8.9530991E-03 0.1859436 at 130iterations 5.0209230E-03 0.1101413 at 140iterations 2.8136531E-03 6.0197115E-02 at 150iterations 1.5756187E-03 3.0362606E-02 at 160iterations 8.8327681E-04 1.7093420E-02 at 170iterations 4.9812515E-04 1.0025024E-02 at 180iterations finished qdiffx linear iterations at : 13:53:42 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 4.9812515E-04 1.0025024E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 13:53:43 13.763u 0.295s 0:16.68 84.2% 0+0k 0+0io 0pf+0w