Sun Oct 9 12:42:28 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 Sun Oct 9 2011 at 12:42:28 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6760607 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): -7.672000 44.24500 ymin,ymax (A): -14.21800 38.44000 zmin,zma (A): 1.100000 44.40900 x,y,z range (A): 51.91700 52.65800 43.30900 scale (grids/A): 0.6760607 object centre (A): 18.28650 12.11100 22.75450 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500026 assigned positive charge : 365.8771 centred at (gu) : 89.97446 90.67950 91.15440 assigned negative charge : -363.3775 centred at (gu) : 89.99149 90.86507 91.21757 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7281 nv = 96 ne = 84 npr = 48238 no. pairs analyzed = 48238 no. exposed pairs = 2936 no. arc points = 21080 no. surface atoms = 992 nbur = 1393 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3999 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.1900000 number of dielectric boundary points 3636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8483 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1944903E-08 -9.3348325E-09 midg,1,midg; midg,igrid,midg 5.2786447E-08 -4.8390888E-08 1,midg,midg; igrid,midg,midg 1.5152109E-08 5.6331912E-09 gauss-seidel spectral radius is 0.9886369 estimated iterations to convergence 77 setup time was (sec) 0.3700000 now iterating at: 12:42:28 rms-change max change #iterations 0.1826038 31.35674 at 10iterations 2.0908482E-02 3.032884 at 20iterations 2.9105088E-03 0.4245682 at 30iterations 6.7568838E-04 0.1083527 at 40iterations 2.2439811E-04 3.6998749E-02 at 50iterations finished qdiffx linear iterations at : 12:42:31 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.2439811E-04 3.6998749E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 12:42:32 3.366u 0.166s 0:03.92 89.7% 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 Sun Oct 9 2011 at 12:42:32 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.028182 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): -7.672000 44.24500 ymin,ymax (A): -14.21800 38.44000 zmin,zma (A): 1.100000 44.40900 x,y,z range (A): 51.91700 52.65800 43.30900 scale (grids/A): 2.028182 object centre (A): 18.28650 12.11100 22.75450 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500026 assigned positive charge : 365.8771 centred at (gu) : 89.92323 92.03804 93.46281 assigned negative charge : -363.3775 centred at (gu) : 89.97427 92.59480 93.65264 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 77756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21080 grid for indexing accessible points = 1.400000 m= 29533 mr = 53722 m= 5007 mr = 22068 m= 406 mr = 3222 m= 7 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2293 time to turn everything in is 0.3800000 number of dielectric boundary points 33484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17749 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) : 0.6760607 object centre at (A) : 18.28650 12.11100 22.75450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9744612E-02 5.6131571E-03 midg,1,midg; midg,igrid,midg 1.6611895E-02 -6.3940488E-02 1,midg,midg; igrid,midg,midg 4.1116826E-02 -1.0582547E-02 gauss-seidel spectral radius is 0.9987714 estimated iterations to convergence 226 setup time was (sec) 0.5800000 now iterating at: 12:42:32 rms-change max change #iterations 4.637980 206.7457 at 10iterations 2.248493 74.29208 at 20iterations 1.095871 35.24637 at 30iterations 0.5357869 16.89321 at 40iterations 0.2599218 8.457863 at 50iterations 0.1266988 3.971631 at 60iterations 6.1940733E-02 1.952316 at 70iterations 3.0317124E-02 0.9147487 at 80iterations 1.4956769E-02 0.4436607 at 90iterations 7.4620196E-03 0.2400007 at 100iterations 3.8022967E-03 0.1325912 at 110iterations 2.0049745E-03 6.4056396E-02 at 120iterations finished qdiffx linear iterations at : 12:42:39 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.0049745E-03 6.4056396E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 12:42:40 7.716u 0.203s 0:08.20 96.4% 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 Sun Oct 9 2011 at 12:42:40 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.042273 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): -7.672000 44.24500 ymin,ymax (A): -14.21800 38.44000 zmin,zma (A): 1.100000 44.40900 x,y,z range (A): 51.91700 52.65800 43.30900 scale (grids/A): 3.042273 object centre (A): 18.28650 12.11100 22.75450 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500026 assigned positive charge : 365.8771 centred at (gu) : 89.88482 93.05694 95.19418 assigned negative charge : -363.3775 centred at (gu) : 89.96133 93.89214 95.47892 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 179228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21080 grid for indexing accessible points = 1.400000 m= 93919 mr = 129691 m= 35733 mr = 77380 m= 9141 mr = 28978 m= 1664 mr = 7020 m= 152 mr = 1233 m= 0 mr = 94 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 7902 time to turn everything in is 1.000000 number of dielectric boundary points 75441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 17943 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) : 2.028182 object centre at (A) : 18.28650 12.11100 22.75450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3885165 -4.6910416E-02 midg,1,midg; midg,igrid,midg 0.4380467 -0.6274694 1,midg,midg; igrid,midg,midg 0.3862322 -0.4007509 gauss-seidel spectral radius is 0.9992830 estimated iterations to convergence 295 setup time was (sec) 1.230000 now iterating at: 12:42:41 rms-change max change #iterations 10.54850 413.6020 at 10iterations 6.183986 136.4027 at 20iterations 3.639788 71.66883 at 30iterations 2.130823 44.45060 at 40iterations 1.244125 23.18941 at 50iterations 0.7266567 12.90685 at 60iterations 0.4234487 7.841659 at 70iterations 0.2471458 4.458732 at 80iterations 0.1438168 2.386784 at 90iterations 8.3907254E-02 1.411987 at 100iterations 4.9052197E-02 1.006275 at 110iterations 2.8766140E-02 0.4844513 at 120iterations 1.7051883E-02 0.3056803 at 130iterations 1.0285317E-02 0.2033882 at 140iterations 6.3985460E-03 0.1416435 at 150iterations 4.1740048E-03 9.2626572E-02 at 160iterations 2.8921175E-03 6.3312531E-02 at 170iterations 2.1267245E-03 5.2093506E-02 at 180iterations finished qdiffx linear iterations at : 12:42:53 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 2.1267245E-03 5.2093506E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 12:42:53 12.585u 0.213s 0:13.07 97.8% 0+0k 0+0io 0pf+0w