Sat Oct 8 16:52:14 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+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 Sat Oct 8 2011 at 16:52:14 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 = 3579 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: 0.5582825 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): 15.47300 79.24000 ymin,ymax (A): 128.0700 183.7730 zmin,zma (A): -1.286000 60.04300 x,y,z range (A): 63.76700 55.70299 61.32900 scale (grids/A): 0.5582825 object centre (A): 47.35650 155.9215 29.37850 number of atom coordinates read : 3579 total number of charged atoms : 3457 net assigned charge : -0.4999836 assigned positive charge : 544.5455 centred at (gu) : 91.41654 89.29030 88.17443 assigned negative charge : -545.0468 centred at (gu) : 91.38497 89.13829 88.21895 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7380 nv = 96 ne = 84 npr = 70129 no. pairs analyzed = 70129 no. exposed pairs = 4766 no. arc points = 33098 no. surface atoms = 1594 nbur = 1985 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 = 1.512000 m= 345 mr = 3749 m= 0 mr = 14 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3371 ## 400 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0813861E-10 -3.9668485E-10 midg,1,midg; midg,igrid,midg -2.4032731E-09 1.5476962E-09 1,midg,midg; igrid,midg,midg -3.2054751E-10 4.9719456E-10 gauss-seidel spectral radius is 0.9835026 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 16:52:15 rms-change max change #iterations 9.1820501E-02 14.13750 at 10iterations 6.4691636E-03 1.044930 at 20iterations 5.1718741E-04 7.8342438E-02 at 30iterations 1.1913086E-04 1.6807079E-02 at 40iterations 5.4344640E-05 7.8170300E-03 at 50iterations finished qdiffx linear iterations at : 16:52:19 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 5.4344640E-05 7.8170300E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 16:52:19 4.187u 0.233s 0:04.92 89.6% 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 Sat Oct 8 2011 at 16:52:19 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 = 3579 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: 1.674847 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): 15.47300 79.24000 ymin,ymax (A): 128.0700 183.7730 zmin,zma (A): -1.286000 60.04300 x,y,z range (A): 63.76700 55.70299 61.32900 scale (grids/A): 1.674847 object centre (A): 47.35650 155.9215 29.37850 number of atom coordinates read : 3579 total number of charged atoms : 3457 net assigned charge : -0.4999836 assigned positive charge : 544.5455 centred at (gu) : 94.24881 87.86999 84.52277 assigned negative charge : -545.0468 centred at (gu) : 94.15447 87.41428 84.65655 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33098 grid for indexing accessible points = 1.400000 m= 25270 mr = 54564 m= 3047 mr = 16862 m= 115 mr = 1573 m= 0 mr = 19 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 36641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 26660 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) : 0.5582825 object centre at (A) : 47.35650 155.9215 29.37850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0769785E-03 9.8982025E-03 midg,1,midg; midg,igrid,midg -1.8289255E-02 2.0449731E-02 1,midg,midg; igrid,midg,midg -1.1605938E-02 -2.0377547E-02 gauss-seidel spectral radius is 0.9983550 estimated iterations to convergence 196 setup time was (sec) 0.9300000 now iterating at: 16:52:20 rms-change max change #iterations 3.933086 156.4919 at 10iterations 1.713444 55.60168 at 20iterations 0.7442257 25.51566 at 30iterations 0.3232397 11.31626 at 40iterations 0.1409641 4.910286 at 50iterations 6.1447240E-02 1.912918 at 60iterations 2.6751067E-02 0.9678698 at 70iterations 1.1696115E-02 0.3830891 at 80iterations 5.1168385E-03 0.1723423 at 90iterations 2.2587487E-03 7.0518017E-02 at 100iterations 1.0210100E-03 3.6644936E-02 at 110iterations 4.9478537E-04 1.7999649E-02 at 120iterations finished qdiffx linear iterations at : 16:52:29 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 4.9478537E-04 1.7999649E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 16:52:29 9.615u 0.245s 0:10.12 97.3% 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 Sat Oct 8 2011 at 16:52:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3579 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: 2.512271 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): 15.47300 79.24000 ymin,ymax (A): 128.0700 183.7730 zmin,zma (A): -1.286000 60.04300 x,y,z range (A): 63.76700 55.70299 61.32900 scale (grids/A): 2.512271 object centre (A): 47.35650 155.9215 29.37850 number of atom coordinates read : 3579 total number of charged atoms : 3457 net assigned charge : -0.4999836 assigned positive charge : 544.5455 centred at (gu) : 96.37298 86.80480 81.78398 assigned negative charge : -545.0468 centred at (gu) : 96.23168 86.12148 81.98469 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 188416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33098 grid for indexing accessible points = 1.400000 m= 86496 mr = 133732 m= 25592 mr = 67168 m= 4907 mr = 18830 m= 454 mr = 3275 m= 11 mr = 243 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 82628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 27644 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) : 1.674847 object centre at (A) : 47.35650 155.9215 29.37850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2157907 0.2645671 midg,1,midg; midg,igrid,midg -0.2667609 0.3198545 1,midg,midg; igrid,midg,midg -0.1981960 -0.3778036 gauss-seidel spectral radius is 0.9992144 estimated iterations to convergence 282 setup time was (sec) 1.820000 now iterating at: 16:52:31 rms-change max change #iterations 10.15845 302.5527 at 10iterations 5.923968 139.7680 at 20iterations 3.436955 73.29619 at 30iterations 1.982447 40.91684 at 40iterations 1.137585 22.65769 at 50iterations 0.6501393 12.55807 at 60iterations 0.3711957 7.340568 at 70iterations 0.2114251 4.113925 at 80iterations 0.1200649 2.303133 at 90iterations 6.8142131E-02 1.508538 at 100iterations 3.8716618E-02 0.7408772 at 110iterations 2.1950047E-02 0.3861606 at 120iterations 1.2420565E-02 0.2249994 at 130iterations 7.0616161E-03 0.1338425 at 140iterations 3.9883936E-03 7.4796677E-02 at 150iterations 2.2632128E-03 3.9085865E-02 at 160iterations 1.2850600E-03 2.3803711E-02 at 170iterations 7.3256076E-04 1.3146162E-02 at 180iterations finished qdiffx linear iterations at : 16:52:45 total time elapsed so far: 15.33000 # loops : 180 mean,max change (kT/e) : 7.3256076E-04 1.3146162E-02 energy calculations done at 15.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.51000 DelPhi exited at 16:52:45 15.508u 0.277s 0:16.05 98.2% 0+0k 0+0io 0pf+0w