Mon Oct 10 14:02:16 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 Mon Oct 10 2011 at 14:02:16 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4505 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: 0.5535858 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): -57.47900 6.811000 ymin,ymax (A): -49.99200 5.170000 zmin,zma (A): -73.79700 -9.488999 x,y,z range (A): 64.29000 55.16200 64.30801 scale (grids/A): 0.5535858 object centre (A): -25.33400 -22.41100 -41.64300 number of atom coordinates read : 4505 total number of charged atoms : 4379 net assigned charge : 10.50004 assigned positive charge : 682.3779 centred at (gu) : 90.24037 90.41917 89.33971 assigned negative charge : -671.8820 centred at (gu) : 90.17347 90.57832 89.43040 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8982 nv = 96 ne = 84 npr = 90705 no. pairs analyzed = 90705 no. exposed pairs = 5398 no. arc points = 36979 no. surface atoms = 1825 nbur = 2680 mkacc time = 0.1600000 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 = 1.568000 m= 353 mr = 4985 m= 0 mr = 21 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3812 ## 505 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 11823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4334434E-09 -2.8409322E-10 midg,1,midg; midg,igrid,midg 2.6653550E-09 -1.4267630E-09 1,midg,midg; igrid,midg,midg -1.5531158E-11 1.8663229E-09 gauss-seidel spectral radius is 0.9832847 estimated iterations to convergence 64 setup time was (sec) 0.4900000 now iterating at: 14:02:17 rms-change max change #iterations 0.1007025 14.27779 at 10iterations 9.6536772E-03 1.341442 at 20iterations 2.2627513E-03 0.2802963 at 30iterations 7.8655820E-04 9.5188141E-02 at 40iterations 2.8971967E-04 3.6909103E-02 at 50iterations finished qdiffx linear iterations at : 14:02:20 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.8971967E-04 3.6909103E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 14:02:20 3.468u 0.165s 0:04.19 86.3% 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 Mon Oct 10 2011 at 14:02:21 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4505 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.660757 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): -57.47900 6.811000 ymin,ymax (A): -49.99200 5.170000 zmin,zma (A): -73.79700 -9.488999 x,y,z range (A): 64.29000 55.16200 64.30801 scale (grids/A): 1.660757 object centre (A): -25.33400 -22.41100 -41.64300 number of atom coordinates read : 4505 total number of charged atoms : 4379 net assigned charge : 10.50004 assigned positive charge : 682.3779 centred at (gu) : 90.71944 91.25610 88.01755 assigned negative charge : -671.8820 centred at (gu) : 90.52005 91.73458 88.29098 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 100291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36979 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 31909 mr = 71128 m= 3295 mr = 22636 m= 117 mr = 1771 m= 0 mr = 22 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 777 time to turn everything in is 0.4700000 number of dielectric boundary points 40055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 459 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33755 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) : 0.5535858 object centre at (A) : -25.33400 -22.41100 -41.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4374423E-02 -4.6879698E-02 midg,1,midg; midg,igrid,midg 2.5649067E-02 -4.8559471E-03 1,midg,midg; igrid,midg,midg -7.2738691E-03 3.4267507E-02 gauss-seidel spectral radius is 0.9983991 estimated iterations to convergence 198 setup time was (sec) 0.6800000 now iterating at: 14:02:21 rms-change max change #iterations 4.377605 179.6916 at 10iterations 1.925118 55.30688 at 20iterations 0.8491406 27.14536 at 30iterations 0.3738607 11.07683 at 40iterations 0.1652565 4.869911 at 50iterations 7.3050566E-02 2.305984 at 60iterations 3.2569546E-02 0.9664288 at 70iterations 1.4849897E-02 0.4566941 at 80iterations 6.9023552E-03 0.2053375 at 90iterations 3.4068259E-03 0.1035538 at 100iterations 1.8487738E-03 5.7533264E-02 at 110iterations 1.0894509E-03 2.8813362E-02 at 120iterations finished qdiffx linear iterations at : 14:02:28 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.0894509E-03 2.8813362E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 14:02:29 7.875u 0.193s 0:08.72 92.4% 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 Mon Oct 10 2011 at 14:02:29 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4505 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: 2.491136 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): -57.47900 6.811000 ymin,ymax (A): -49.99200 5.170000 zmin,zma (A): -73.79700 -9.488999 x,y,z range (A): 64.29000 55.16200 64.30801 scale (grids/A): 2.491136 object centre (A): -25.33400 -22.41100 -41.64300 number of atom coordinates read : 4505 total number of charged atoms : 4379 net assigned charge : 10.50004 assigned positive charge : 682.3779 centred at (gu) : 91.07915 91.88387 87.02601 assigned negative charge : -671.8820 centred at (gu) : 90.78000 92.60196 87.43652 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 233259 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36979 grid for indexing accessible points = 1.400000 m= 110706 mr = 173287 m= 31507 mr = 89274 m= 5179 mr = 24216 m= 420 mr = 3599 m= 19 mr = 236 m= 0 mr = 3 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2627 time to turn everything in is 1.150000 number of dielectric boundary points 90475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 35002 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) : 1.660757 object centre at (A) : -25.33400 -22.41100 -41.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7344192 -0.9472278 midg,1,midg; midg,igrid,midg 0.2924462 -7.2393917E-02 1,midg,midg; igrid,midg,midg -8.6911656E-02 0.5407675 gauss-seidel spectral radius is 0.9992351 estimated iterations to convergence 285 setup time was (sec) 1.390000 now iterating at: 14:02:31 rms-change max change #iterations 11.20280 347.7780 at 10iterations 6.589440 132.9116 at 20iterations 3.848993 89.70043 at 30iterations 2.232998 41.58739 at 40iterations 1.293291 27.73797 at 50iterations 0.7454283 12.85733 at 60iterations 0.4295013 9.137720 at 70iterations 0.2463564 4.603919 at 80iterations 0.1415049 2.577919 at 90iterations 8.1115454E-02 1.372284 at 100iterations 4.6460200E-02 0.8451138 at 110iterations 2.6660511E-02 0.4426689 at 120iterations 1.5314037E-02 0.2873611 at 130iterations 8.7986384E-03 0.1440125 at 140iterations 5.1193098E-03 8.7654114E-02 at 150iterations 3.0070571E-03 4.9289703E-02 at 160iterations 1.7983993E-03 3.0807495E-02 at 170iterations 1.1111875E-03 1.8859863E-02 at 180iterations finished qdiffx linear iterations at : 14:02:42 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 1.1111875E-03 1.8859863E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 14:02:43 13.050u 0.214s 0:13.86 95.6% 0+0k 0+0io 0pf+0w