Mon Oct 10 14:38:50 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 14:38:50 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5679824 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): 7.704999 62.61200 ymin,ymax (A): -26.32000 34.54700 zmin,zma (A): -29.31300 33.36500 x,y,z range (A): 54.90701 60.86700 62.67800 scale (grids/A): 0.5679824 object centre (A): 35.15850 4.113501 2.026001 number of atom coordinates read : 4282 total number of charged atoms : 4159 net assigned charge : 3.500023 assigned positive charge : 639.8275 centred at (gu) : 89.97386 89.94683 89.58419 assigned negative charge : -636.3303 centred at (gu) : 90.00230 89.98357 89.66824 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9136 nv = 96 ne = 84 npr = 86415 no. pairs analyzed = 86415 no. exposed pairs = 5536 no. arc points = 36896 no. surface atoms = 1857 nbur = 2425 mkacc time = 0.2800000 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= 441 mr = 5002 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.6000000 number of dielectric boundary points 4549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3763 ## 389 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 11809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4741660E-09 -1.1657137E-09 midg,1,midg; midg,igrid,midg 1.2753368E-09 -2.7971930E-10 1,midg,midg; igrid,midg,midg 1.0932233E-09 -1.0728936E-10 gauss-seidel spectral radius is 0.9841073 estimated iterations to convergence 65 setup time was (sec) 0.9600000 now iterating at: 14:38:51 rms-change max change #iterations 0.1091628 13.56372 at 10iterations 9.2368647E-03 1.405533 at 20iterations 2.2717332E-03 0.2367744 at 30iterations 1.0653526E-03 0.1103802 at 40iterations 5.2950688E-04 5.6314468E-02 at 50iterations finished qdiffx linear iterations at : 14:38:55 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 5.2950688E-04 5.6314468E-02 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.910000 DelPhi exited at 14:38:56 4.913u 0.419s 0:06.21 85.6% 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 14:38:56 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.703947 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): 7.704999 62.61200 ymin,ymax (A): -26.32000 34.54700 zmin,zma (A): -29.31300 33.36500 x,y,z range (A): 54.90701 60.86700 62.67800 scale (grids/A): 1.703947 object centre (A): 35.15850 4.113501 2.026001 number of atom coordinates read : 4282 total number of charged atoms : 4159 net assigned charge : 3.500023 assigned positive charge : 639.8275 centred at (gu) : 89.92028 89.83916 88.75135 assigned negative charge : -636.3303 centred at (gu) : 90.00668 89.95023 89.00401 start vw surface at 0.2100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 100940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36896 grid for indexing accessible points = 1.400000 m= 34953 mr = 71402 m= 4472 mr = 24820 m= 163 mr = 2375 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 41906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 353 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 32196 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) : 0.5679824 object centre at (A) : 35.15850 4.113501 2.026001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5174474E-02 -1.9679995E-02 midg,1,midg; midg,igrid,midg 2.5905313E-02 1.0965682E-03 1,midg,midg; igrid,midg,midg 5.9704855E-03 6.9021308E-03 gauss-seidel spectral radius is 0.9984760 estimated iterations to convergence 203 setup time was (sec) 1.390000 now iterating at: 14:38:58 rms-change max change #iterations 4.459205 162.2828 at 10iterations 2.006346 61.34097 at 20iterations 0.8985579 27.02715 at 30iterations 0.4046972 11.25496 at 40iterations 0.1818217 4.933934 at 50iterations 8.2057633E-02 2.296310 at 60iterations 3.7251025E-02 0.9985117 at 70iterations 1.7335178E-02 0.4594545 at 80iterations 8.4617706E-03 0.2466812 at 90iterations 4.5742369E-03 0.1278839 at 100iterations 2.8541170E-03 8.7894440E-02 at 110iterations 2.0157893E-03 5.1252365E-02 at 120iterations finished qdiffx linear iterations at : 14:39:10 total time elapsed so far: 13.32000 # loops : 120 mean,max change (kT/e) : 2.0157893E-03 5.1252365E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 14:39:11 13.536u 0.486s 0:14.82 94.5% 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 14:39:11 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.555921 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): 7.704999 62.61200 ymin,ymax (A): -26.32000 34.54700 zmin,zma (A): -29.31300 33.36500 x,y,z range (A): 54.90701 60.86700 62.67800 scale (grids/A): 2.555921 object centre (A): 35.15850 4.113501 2.026001 number of atom coordinates read : 4282 total number of charged atoms : 4159 net assigned charge : 3.500023 assigned positive charge : 639.8275 centred at (gu) : 89.87998 89.75835 88.12665 assigned negative charge : -636.3303 centred at (gu) : 90.00981 89.92536 88.50601 start vw surface at 0.2100000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 234303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36896 grid for indexing accessible points = 1.400000 m= 116634 mr = 174269 m= 38233 mr = 93549 m= 7381 mr = 29458 m= 682 mr = 5122 m= 13 mr = 340 m= 0 mr = 0 time to grow re-entrant surface = 1.660000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.640000 number of dielectric boundary points 94508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 2.810000 number of grid points assigned charge 33257 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) : 1.703947 object centre at (A) : 35.15850 4.113501 2.026001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2729439 -0.3188157 midg,1,midg; midg,igrid,midg 0.4738773 -3.2914687E-02 1,midg,midg; igrid,midg,midg 0.1173607 0.1721454 gauss-seidel spectral radius is 0.9992595 estimated iterations to convergence 290 setup time was (sec) 3.030000 now iterating at: 14:39:15 rms-change max change #iterations 11.41852 287.4915 at 10iterations 6.841807 148.0405 at 20iterations 4.062835 79.72669 at 30iterations 2.392107 48.32742 at 40iterations 1.403743 23.72672 at 50iterations 0.8204033 14.53321 at 60iterations 0.4789436 8.422079 at 70iterations 0.2782954 4.875189 at 80iterations 0.1617055 3.054702 at 90iterations 9.3852296E-02 1.722466 at 100iterations 5.4483041E-02 0.9240303 at 110iterations 3.1652480E-02 0.5305891 at 120iterations 1.8508464E-02 0.3095640 at 130iterations 1.0927689E-02 0.1933141 at 140iterations 6.5895165E-03 0.1092567 at 150iterations 4.1498411E-03 6.9637299E-02 at 160iterations 2.7713240E-03 4.3910980E-02 at 170iterations 2.0001708E-03 2.9027939E-02 at 180iterations finished qdiffx linear iterations at : 14:39:31 total time elapsed so far: 19.82000 # loops : 180 mean,max change (kT/e) : 2.0001708E-03 2.9027939E-02 energy calculations done at 19.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.03000 DelPhi exited at 14:39:32 20.037u 0.500s 0:21.16 97.0% 0+0k 0+0io 0pf+0w