Sun Oct 9 21:05:19 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 Sun Oct 9 2011 at 21:05:19 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 = 3194 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5837022 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): -8.867001 49.73900 ymin,ymax (A): 23.17400 84.16400 zmin,zma (A): -5.057000 47.29400 x,y,z range (A): 58.60600 60.99000 52.35100 scale (grids/A): 0.5837022 object centre (A): 20.43600 53.66900 21.11850 number of atom coordinates read : 3194 total number of charged atoms : 3045 net assigned charge : 3.500013 assigned positive charge : 483.3317 centred at (gu) : 90.72357 89.26716 89.47958 assigned negative charge : -479.8331 centred at (gu) : 90.78256 89.16574 89.45921 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7225 nv = 96 ne = 84 npr = 62882 no. pairs analyzed = 62882 no. exposed pairs = 4010 no. arc points = 28992 no. surface atoms = 1342 nbur = 1852 mkacc time = 0.1400000 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= 335 mr = 3793 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3300000 number of dielectric boundary points 3743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2909 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9150 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0242915E-10 1.2902406E-09 midg,1,midg; midg,igrid,midg -2.2049016E-09 3.0311653E-09 1,midg,midg; igrid,midg,midg 2.0965230E-09 -8.2197704E-10 gauss-seidel spectral radius is 0.9848717 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 21:05:20 rms-change max change #iterations 0.1081918 16.55163 at 10iterations 8.4628481E-03 1.440666 at 20iterations 6.7788950E-04 0.1160507 at 30iterations 5.5691205E-05 7.7667236E-03 at 40iterations 5.4052543E-06 8.0680847E-04 at 50iterations finished qdiffx linear iterations at : 21:05:22 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.4052543E-06 8.0680847E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 21:05:23 3.443u 0.196s 0:03.91 92.8% 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 Sun Oct 9 2011 at 21:05:23 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 = 3194 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.751107 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): -8.867001 49.73900 ymin,ymax (A): 23.17400 84.16400 zmin,zma (A): -5.057000 47.29400 x,y,z range (A): 58.60600 60.99000 52.35100 scale (grids/A): 1.751107 object centre (A): 20.43600 53.66900 21.11850 number of atom coordinates read : 3194 total number of charged atoms : 3045 net assigned charge : 3.500013 assigned positive charge : 483.3317 centred at (gu) : 92.17028 87.80035 88.43841 assigned negative charge : -479.8331 centred at (gu) : 92.34724 87.49705 88.37753 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28992 grid for indexing accessible points = 1.400000 m= 25541 mr = 53561 m= 3368 mr = 17827 m= 158 mr = 1918 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1197 time to turn everything in is 0.5400000 number of dielectric boundary points 34591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 23671 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) : 0.5837022 object centre at (A) : 20.43600 53.66900 21.11850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9149433E-03 2.8825493E-03 midg,1,midg; midg,igrid,midg -1.4009278E-02 -1.4322730E-02 1,midg,midg; igrid,midg,midg -5.2948808E-03 3.6381839E-03 gauss-seidel spectral radius is 0.9984610 estimated iterations to convergence 202 setup time was (sec) 0.8500000 now iterating at: 21:05:24 rms-change max change #iterations 4.000133 180.0781 at 10iterations 1.771814 59.93372 at 20iterations 0.7898351 26.24890 at 30iterations 0.3533017 11.77401 at 40iterations 0.1575683 5.459671 at 50iterations 7.0446633E-02 2.236643 at 60iterations 3.1323079E-02 1.063419 at 70iterations 1.3999854E-02 0.4454777 at 80iterations 6.2743262E-03 0.1936464 at 90iterations 2.8015207E-03 9.0507507E-02 at 100iterations 1.2524130E-03 4.0462971E-02 at 110iterations 5.6059298E-04 1.7562866E-02 at 120iterations finished qdiffx linear iterations at : 21:05:31 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 5.6059298E-04 1.7562866E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 21:05:31 7.706u 0.244s 0:08.23 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 21:05:31 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 = 3194 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.626660 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): -8.867001 49.73900 ymin,ymax (A): 23.17400 84.16400 zmin,zma (A): -5.057000 47.29400 x,y,z range (A): 58.60600 60.99000 52.35100 scale (grids/A): 2.626660 object centre (A): 20.43600 53.66900 21.11850 number of atom coordinates read : 3194 total number of charged atoms : 3045 net assigned charge : 3.500013 assigned positive charge : 483.3317 centred at (gu) : 93.25509 86.70021 87.65737 assigned negative charge : -479.8331 centred at (gu) : 93.52081 86.24531 87.56629 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 183006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28992 grid for indexing accessible points = 1.400000 m= 85794 mr = 130922 m= 27118 mr = 68282 m= 5668 mr = 20708 m= 651 mr = 3952 m= 27 mr = 372 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 4042 time to turn everything in is 1.340000 number of dielectric boundary points 78026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 24346 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) : 1.751107 object centre at (A) : 20.43600 53.66900 21.11850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7685270E-02 2.8362481E-02 midg,1,midg; midg,igrid,midg -0.2859472 -0.2755227 1,midg,midg; igrid,midg,midg -0.1922410 -6.4619906E-02 gauss-seidel spectral radius is 0.9992257 estimated iterations to convergence 284 setup time was (sec) 1.660000 now iterating at: 21:05:33 rms-change max change #iterations 9.944472 357.4590 at 10iterations 5.808687 142.9515 at 20iterations 3.344577 72.82042 at 30iterations 1.928600 40.21624 at 40iterations 1.104411 25.00922 at 50iterations 0.6327878 12.87460 at 60iterations 0.3617795 7.838798 at 70iterations 0.2061911 3.900070 at 80iterations 0.1175272 2.259604 at 90iterations 6.7003369E-02 1.277131 at 100iterations 3.8013063E-02 0.6750097 at 110iterations 2.1620503E-02 0.4698410 at 120iterations 1.2301203E-02 0.2070503 at 130iterations 6.9717015E-03 0.1478052 at 140iterations 3.9668130E-03 7.2057724E-02 at 150iterations 2.2515180E-03 4.3634415E-02 at 160iterations 1.2778920E-03 2.2855759E-02 at 170iterations 7.2646677E-04 1.3980865E-02 at 180iterations finished qdiffx linear iterations at : 21:05:44 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 7.2646677E-04 1.3980865E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 21:05:44 12.425u 0.259s 0:12.95 97.8% 0+0k 0+0io 0pf+0w