Mon Oct 10 14:17:56 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 14:17:56 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5947111 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): -45.61300 5.513000 ymin,ymax (A): -43.36100 16.50000 zmin,zma (A): 40.03800 90.56800 x,y,z range (A): 51.12600 59.86100 50.53000 scale (grids/A): 0.5947111 object centre (A): -20.05000 -13.43050 65.30300 number of atom coordinates read : 2725 total number of charged atoms : 2581 net assigned charge : -5.999987 assigned positive charge : 418.6975 centred at (gu) : 90.98071 87.31283 89.12818 assigned negative charge : -424.6983 centred at (gu) : 90.88571 87.27454 89.17365 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6525 nv = 96 ne = 84 npr = 53372 no. pairs analyzed = 53372 no. exposed pairs = 3791 no. arc points = 26051 no. surface atoms = 1287 nbur = 1438 mkacc time = 0.1500000 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= 341 mr = 3307 m= 2 mr = 41 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 0.3900000 number of dielectric boundary points 3520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2718 ## 299 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.4897705E-10 -3.0227925E-09 midg,1,midg; midg,igrid,midg -6.3646652E-09 -5.0626386E-10 1,midg,midg; igrid,midg,midg -4.2927835E-09 1.2875819E-09 gauss-seidel spectral radius is 0.9853867 estimated iterations to convergence 68 setup time was (sec) 0.6400000 now iterating at: 14:17:57 rms-change max change #iterations 0.1092922 16.23379 at 10iterations 8.7574320E-03 1.321456 at 20iterations 7.5437821E-04 0.1244049 at 30iterations 7.7197699E-05 1.3038635E-02 at 40iterations 1.4030913E-05 2.6092529E-03 at 50iterations finished qdiffx linear iterations at : 14:17:59 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.4030913E-05 2.6092529E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 14:18:00 3.474u 0.199s 0:04.13 88.6% 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 14:18:00 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.784133 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): -45.61300 5.513000 ymin,ymax (A): -43.36100 16.50000 zmin,zma (A): 40.03800 90.56800 x,y,z range (A): 51.12600 59.86100 50.53000 scale (grids/A): 1.784133 object centre (A): -20.05000 -13.43050 65.30300 number of atom coordinates read : 2725 total number of charged atoms : 2581 net assigned charge : -5.999987 assigned positive charge : 418.6975 centred at (gu) : 92.94154 81.93792 87.38370 assigned negative charge : -424.6983 centred at (gu) : 92.65683 81.82340 87.52081 start vw surface at 0.2200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 70455 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26051 grid for indexing accessible points = 1.400000 m= 24478 mr = 47002 m= 3777 mr = 16997 m= 192 mr = 2211 m= 0 mr = 57 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 32635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20139 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) : 0.5947111 object centre at (A) : -20.05000 -13.43050 65.30300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8857570E-02 -1.3605962E-02 midg,1,midg; midg,igrid,midg -3.8325676E-04 3.3820346E-02 1,midg,midg; igrid,midg,midg -2.4873341E-02 -1.1363101E-02 gauss-seidel spectral radius is 0.9984697 estimated iterations to convergence 203 setup time was (sec) 0.9300000 now iterating at: 14:18:01 rms-change max change #iterations 3.966568 176.4219 at 10iterations 1.761142 67.25566 at 20iterations 0.7885440 31.71434 at 30iterations 0.3540451 14.26263 at 40iterations 0.1582378 5.158515 at 50iterations 7.0820853E-02 2.413170 at 60iterations 3.1728424E-02 1.017395 at 70iterations 1.4223090E-02 0.4352102 at 80iterations 6.3629802E-03 0.2194271 at 90iterations 2.8484736E-03 0.1015453 at 100iterations 1.2769133E-03 4.4044495E-02 at 110iterations 5.7616644E-04 2.1245956E-02 at 120iterations finished qdiffx linear iterations at : 14:18:08 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 5.7616644E-04 2.1245956E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 14:18:08 7.540u 0.229s 0:08.23 94.2% 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 14:18:08 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 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: 2.676200 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): -45.61300 5.513000 ymin,ymax (A): -43.36100 16.50000 zmin,zma (A): 40.03800 90.56800 x,y,z range (A): 51.12600 59.86100 50.53000 scale (grids/A): 2.676200 object centre (A): -20.05000 -13.43050 65.30300 number of atom coordinates read : 2725 total number of charged atoms : 2581 net assigned charge : -5.999987 assigned positive charge : 418.6975 centred at (gu) : 94.41216 77.90663 86.07537 assigned negative charge : -424.6983 centred at (gu) : 93.98509 77.73505 86.28109 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 162818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26051 grid for indexing accessible points = 1.400000 m= 79846 mr = 114754 m= 27692 mr = 62873 m= 6608 mr = 21299 m= 910 mr = 4804 m= 47 mr = 579 m= 0 mr = 19 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 73593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 20637 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) : 1.784133 object centre at (A) : -20.05000 -13.43050 65.30300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2688166 -0.1342112 midg,1,midg; midg,igrid,midg -0.2350878 0.5923280 1,midg,midg; igrid,midg,midg -0.3181023 -0.1042956 gauss-seidel spectral radius is 0.9992231 estimated iterations to convergence 283 setup time was (sec) 1.600000 now iterating at: 14:18:10 rms-change max change #iterations 9.745233 312.2603 at 10iterations 5.740144 145.2051 at 20iterations 3.322084 81.50924 at 30iterations 1.921796 38.57132 at 40iterations 1.101491 21.51819 at 50iterations 0.6297395 12.47219 at 60iterations 0.3593727 7.364103 at 70iterations 0.2050150 3.886460 at 80iterations 0.1166274 2.410772 at 90iterations 6.6447072E-02 1.339331 at 100iterations 3.7733380E-02 0.7928658 at 110iterations 2.1329599E-02 0.4137402 at 120iterations 1.2149553E-02 0.2537838 at 130iterations 6.8972488E-03 0.1321945 at 140iterations 3.9072004E-03 7.6757431E-02 at 150iterations 2.2156565E-03 4.3426514E-02 at 160iterations 1.2559758E-03 2.5876045E-02 at 170iterations 7.1147003E-04 1.3941765E-02 at 180iterations finished qdiffx linear iterations at : 14:18:20 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 7.1147003E-04 1.3941765E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 14:18:20 11.621u 0.210s 0:12.16 97.2% 0+0k 0+0io 0pf+0w