Tue Oct 11 07:36:46 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 Tue Oct 11 2011 at 07:36:46 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 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: 0.6472610 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): -10.62400 39.93000 ymin,ymax (A): -14.35700 40.64400 zmin,zma (A): 7.324000 52.17400 x,y,z range (A): 50.55400 55.00100 44.85000 scale (grids/A): 0.6472610 object centre (A): 14.65300 13.14350 29.74900 number of atom coordinates read : 2377 total number of charged atoms : 2241 net assigned charge : 4.500007 assigned positive charge : 358.5564 centred at (gu) : 89.89463 88.35690 90.32708 assigned negative charge : -354.0567 centred at (gu) : 89.82468 88.34821 90.47516 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6593 nv = 96 ne = 84 npr = 48316 no. pairs analyzed = 48316 no. exposed pairs = 2938 no. arc points = 20143 no. surface atoms = 998 nbur = 1379 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 3628 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1981 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7857 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5149227E-08 -1.2127578E-08 midg,1,midg; midg,igrid,midg 9.8374437E-09 6.6307000E-09 1,midg,midg; igrid,midg,midg -9.7550845E-10 1.6732825E-08 gauss-seidel spectral radius is 0.9876085 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 07:36:46 rms-change max change #iterations 0.1488256 23.93356 at 10iterations 1.5310309E-02 2.254436 at 20iterations 1.5400557E-03 0.2245655 at 30iterations 1.6386804E-04 2.4591446E-02 at 40iterations 2.0762798E-05 2.7713776E-03 at 50iterations finished qdiffx linear iterations at : 07:36:49 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.0762798E-05 2.7713776E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 07:36:50 3.335u 0.166s 0:04.09 85.3% 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 Tue Oct 11 2011 at 07:36:50 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 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: 1.941783 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): -10.62400 39.93000 ymin,ymax (A): -14.35700 40.64400 zmin,zma (A): 7.324000 52.17400 x,y,z range (A): 50.55400 55.00100 44.85000 scale (grids/A): 1.941783 object centre (A): 14.65300 13.14350 29.74900 number of atom coordinates read : 2377 total number of charged atoms : 2241 net assigned charge : 4.500007 assigned positive charge : 358.5564 centred at (gu) : 89.68370 85.07020 90.98097 assigned negative charge : -354.0567 centred at (gu) : 89.47380 85.04459 91.42524 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20143 grid for indexing accessible points = 1.400000 m= 27973 mr = 48420 m= 5015 mr = 21129 m= 286 mr = 3237 m= 1 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 30437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17633 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) : 0.6472610 object centre at (A) : 14.65300 13.14350 29.74900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1678274E-02 -2.5065724E-02 midg,1,midg; midg,igrid,midg 1.0880345E-02 3.8886756E-02 1,midg,midg; igrid,midg,midg -3.4896468E-03 6.2163612E-03 gauss-seidel spectral radius is 0.9986608 estimated iterations to convergence 217 setup time was (sec) 0.5800000 now iterating at: 07:36:51 rms-change max change #iterations 4.201336 172.6603 at 10iterations 1.988222 83.44064 at 20iterations 0.9407820 31.51377 at 30iterations 0.4441083 13.71767 at 40iterations 0.2101292 7.497782 at 50iterations 9.9401787E-02 3.277105 at 60iterations 4.6895586E-02 1.564857 at 70iterations 2.2162911E-02 0.6837578 at 80iterations 1.0467188E-02 0.3513145 at 90iterations 4.9610813E-03 0.1441879 at 100iterations 2.3417363E-03 7.9021454E-02 at 110iterations 1.1160028E-03 3.8985252E-02 at 120iterations finished qdiffx linear iterations at : 07:36:58 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.1160028E-03 3.8985252E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 07:36:58 7.709u 0.173s 0:08.21 95.8% 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 Tue Oct 11 2011 at 07:36:58 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 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: 2.912674 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): -10.62400 39.93000 ymin,ymax (A): -14.35700 40.64400 zmin,zma (A): 7.324000 52.17400 x,y,z range (A): 50.55400 55.00100 44.85000 scale (grids/A): 2.912674 object centre (A): 14.65300 13.14350 29.74900 number of atom coordinates read : 2377 total number of charged atoms : 2241 net assigned charge : 4.500007 assigned positive charge : 358.5564 centred at (gu) : 89.52533 82.60529 91.47136 assigned negative charge : -354.0567 centred at (gu) : 89.21066 82.56685 92.13782 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20143 grid for indexing accessible points = 1.400000 m= 86636 mr = 116606 m= 35461 mr = 71631 m= 9356 mr = 29105 m= 1381 mr = 7155 m= 55 mr = 920 m= 0 mr = 25 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 68565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 17923 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) : 1.941783 object centre at (A) : 14.65300 13.14350 29.74900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3795365 -0.3355366 midg,1,midg; midg,igrid,midg -0.1985397 0.4317677 1,midg,midg; igrid,midg,midg -4.3799672E-02 8.5539343E-03 gauss-seidel spectral radius is 0.9992594 estimated iterations to convergence 290 setup time was (sec) 1.170000 now iterating at: 07:37:00 rms-change max change #iterations 9.671184 348.2410 at 10iterations 5.641338 130.9370 at 20iterations 3.278947 68.29645 at 30iterations 1.897866 36.31468 at 40iterations 1.096121 24.48995 at 50iterations 0.6335132 11.68987 at 60iterations 0.3656236 7.726148 at 70iterations 0.2106229 4.291672 at 80iterations 0.1214790 2.371351 at 90iterations 6.9762595E-02 1.446549 at 100iterations 4.0191475E-02 0.7491001 at 110iterations 2.3131365E-02 0.4462032 at 120iterations 1.3304248E-02 0.2441940 at 130iterations 7.6562138E-03 0.1383376 at 140iterations 4.4059078E-03 8.1798553E-02 at 150iterations 2.5397730E-03 4.7077179E-02 at 160iterations 1.4677662E-03 2.7618408E-02 at 170iterations 8.5181720E-04 1.5805721E-02 at 180iterations finished qdiffx linear iterations at : 07:37:11 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 8.5181720E-04 1.5805721E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 07:37:11 12.447u 0.203s 0:12.94 97.6% 0+0k 0+0io 0pf+0w