Wed Dec 21 14:21:39 PST 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 Wed Dec 21 2011 at 14:21:41 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 = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6008337 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): -34.65200 13.12800 ymin,ymax (A): 0.4220001 41.02900 zmin,zma (A): -0.1589999 59.09200 x,y,z range (A): 47.78000 40.60700 59.25100 scale (grids/A): 0.6008337 object centre (A): -10.76200 20.72550 29.46650 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 4.000004 assigned positive charge : 285.3821 centred at (gu) : 89.43581 89.79102 89.05994 assigned negative charge : -281.3823 centred at (gu) : 89.31419 89.97405 89.03449 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4811 nv = 96 ne = 84 npr = 39703 no. pairs analyzed = 39703 no. exposed pairs = 2451 no. arc points = 17318 no. surface atoms = 838 nbur = 1108 mkacc time = 0.1300000 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 = 1.456000 m= 230 mr = 2632 m= 0 mr = 18 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1743 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 5830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3325766E-09 2.0070345E-09 midg,1,midg; midg,igrid,midg 6.9682282E-09 -3.1286331E-09 1,midg,midg; igrid,midg,midg -1.7946288E-09 4.4330943E-09 gauss-seidel spectral radius is 0.9856094 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 14:21:43 rms-change max change #iterations 9.1029741E-02 15.43650 at 10iterations 7.4778227E-03 1.486783 at 20iterations 6.3524948E-04 9.9594116E-02 at 30iterations 5.5515575E-05 1.1834145E-02 at 40iterations 4.6585546E-06 7.7724457E-04 at 50iterations finished qdiffx linear iterations at : 14:21:49 total time elapsed so far: 6.960000 # loops : 50 mean,max change (kT/e) : 4.6585546E-06 7.7724457E-04 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 14:22:02 7.189u 0.575s 0:22.61 34.2% 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 Wed Dec 21 2011 at 14:22:05 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 = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.802501 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): -34.65200 13.12800 ymin,ymax (A): 0.4220001 41.02900 zmin,zma (A): -0.1589999 59.09200 x,y,z range (A): 47.78000 40.60700 59.25100 scale (grids/A): 1.802501 object centre (A): -10.76200 20.72550 29.46650 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 4.000004 assigned positive charge : 285.3821 centred at (gu) : 88.30746 89.37320 87.17984 assigned negative charge : -281.3823 centred at (gu) : 87.94271 89.92242 87.10372 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 52105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17318 grid for indexing accessible points = 1.400000 m= 18700 mr = 35801 m= 2514 mr = 13975 m= 100 mr = 1480 m= 0 mr = 23 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 22140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14197 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) : 0.6008337 object centre at (A) : -10.76200 20.72550 29.46650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6875830E-02 2.3139820E-02 midg,1,midg; midg,igrid,midg 1.0173500E-02 -9.7207250E-03 1,midg,midg; igrid,midg,midg -4.0725758E-03 2.8719765E-03 gauss-seidel spectral radius is 0.9984013 estimated iterations to convergence 198 setup time was (sec) 1.040000 now iterating at: 14:22:07 rms-change max change #iterations 3.162116 153.3306 at 10iterations 1.387161 55.38945 at 20iterations 0.6091746 24.38246 at 30iterations 0.2684519 10.98576 at 40iterations 0.1177484 4.574297 at 50iterations 5.1803928E-02 1.909006 at 60iterations 2.2681529E-02 0.8816376 at 70iterations 9.9547254E-03 0.3491306 at 80iterations 4.4106930E-03 0.1672421 at 90iterations 1.9411584E-03 7.3077202E-02 at 100iterations 8.5280143E-04 3.0881882E-02 at 110iterations 3.7402156E-04 1.3912201E-02 at 120iterations finished qdiffx linear iterations at : 14:22:23 total time elapsed so far: 16.67000 # loops : 120 mean,max change (kT/e) : 3.7402156E-04 1.3912201E-02 energy calculations done at 16.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.88000 DelPhi exited at 14:22:33 16.882u 0.629s 0:28.69 60.9% 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 Wed Dec 21 2011 at 14:22:35 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 = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.703752 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): -34.65200 13.12800 ymin,ymax (A): 0.4220001 41.02900 zmin,zma (A): -0.1589999 59.09200 x,y,z range (A): 47.78000 40.60700 59.25100 scale (grids/A): 2.703752 object centre (A): -10.76200 20.72550 29.46650 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 4.000004 assigned positive charge : 285.3821 centred at (gu) : 87.46135 89.05990 85.76979 assigned negative charge : -281.3823 centred at (gu) : 86.91402 89.88368 85.65549 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 120613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17318 grid for indexing accessible points = 1.400000 m= 61089 mr = 86703 m= 21035 mr = 50382 m= 4341 mr = 17163 m= 398 mr = 3154 m= 16 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 49873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 14527 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) : 1.802501 object centre at (A) : -10.76200 20.72550 29.46650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1361785 0.2259706 midg,1,midg; midg,igrid,midg 8.4319688E-02 -0.1364888 1,midg,midg; igrid,midg,midg -7.9267479E-02 3.5032600E-02 gauss-seidel spectral radius is 0.9991738 estimated iterations to convergence 275 setup time was (sec) 2.000000 now iterating at: 14:22:38 rms-change max change #iterations 7.555801 275.2954 at 10iterations 4.243689 132.5213 at 20iterations 2.372122 53.78627 at 30iterations 1.320906 29.33483 at 40iterations 0.7340059 15.93823 at 50iterations 0.4070392 9.243132 at 60iterations 0.2256531 5.098502 at 70iterations 0.1256125 2.575769 at 80iterations 6.9621846E-02 1.619240 at 90iterations 3.8559381E-02 0.8922670 at 100iterations 2.1489814E-02 0.4517269 at 110iterations 1.1912534E-02 0.2526903 at 120iterations 6.6255312E-03 0.1660843 at 130iterations 3.6716512E-03 7.6217651E-02 at 140iterations 2.0418216E-03 4.0951252E-02 at 150iterations 1.1322187E-03 2.4956822E-02 at 160iterations 6.2891317E-04 1.3587952E-02 at 170iterations 3.4892920E-04 7.6513290E-03 at 180iterations finished qdiffx linear iterations at : 14:23:04 total time elapsed so far: 28.05000 # loops : 180 mean,max change (kT/e) : 3.4892920E-04 7.6513290E-03 energy calculations done at 28.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.27000 DelPhi exited at 14:23:07 28.277u 0.793s 0:32.46 89.5% 0+0k 0+0io 0pf+0w