Mon Oct 10 11:50:46 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 Mon Oct 10 2011 at 11:50:46 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: GLU 223 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7487959 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): -21.82700 24.42400 ymin,ymax (A): 9.141000 53.89600 zmin,zma (A): 5.166000 52.70900 x,y,z range (A): 46.25100 44.75500 47.54300 scale (grids/A): 0.7487959 object centre (A): 1.298500 31.51850 28.93750 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.999990 assigned positive charge : 316.0119 centred at (gu) : 89.25753 89.57068 89.81887 assigned negative charge : -322.0120 centred at (gu) : 89.23590 89.49189 89.67905 start vw surface at 0.1300000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8070 nv = 96 ne = 84 npr = 43806 no. pairs analyzed = 43806 no. exposed pairs = 2686 no. arc points = 18764 no. surface atoms = 915 nbur = 1192 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 593 mr = 4482 m= 4 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3000000 number of dielectric boundary points 4068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1495 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8509 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0949136E-07 4.0224524E-08 midg,1,midg; midg,igrid,midg -2.4158396E-07 -2.9198015E-08 1,midg,midg; igrid,midg,midg -1.7483484E-07 -8.7951960E-08 gauss-seidel spectral radius is 0.9907032 estimated iterations to convergence 84 setup time was (sec) 0.5700000 now iterating at: 11:50:46 rms-change max change #iterations 0.2577939 32.55142 at 10iterations 3.5584092E-02 4.568952 at 20iterations 4.8609199E-03 0.6953735 at 30iterations 6.7394017E-04 8.4376454E-02 at 40iterations 9.2364520E-05 1.1550903E-02 at 50iterations finished qdiffx linear iterations at : 11:50:50 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 9.2364520E-05 1.1550903E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 11:50:50 4.026u 0.268s 0:04.74 90.2% 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 11:50:50 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: GLU 223 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.246387 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): -21.82700 24.42400 ymin,ymax (A): 9.141000 53.89600 zmin,zma (A): 5.166000 52.70900 x,y,z range (A): 46.25100 44.75500 47.54300 scale (grids/A): 2.246387 object centre (A): 1.298500 31.51850 28.93750 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.999990 assigned positive charge : 316.0119 centred at (gu) : 87.77257 88.71186 89.45660 assigned negative charge : -322.0120 centred at (gu) : 87.70778 88.47564 89.03725 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 84451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18764 grid for indexing accessible points = 1.400000 m= 33863 mr = 58210 m= 7533 mr = 25588 m= 839 mr = 5293 m= 24 mr = 431 m= 0 mr = 9 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 835 time to turn everything in is 0.7800000 number of dielectric boundary points 37179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 15702 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) : 0.7487959 object centre at (A) : 1.298500 31.51850 28.93750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1433810 1.1948114E-02 midg,1,midg; midg,igrid,midg -3.9662085E-02 -2.9638296E-02 1,midg,midg; igrid,midg,midg -1.1453651E-02 7.0720953E-03 gauss-seidel spectral radius is 0.9989460 estimated iterations to convergence 244 setup time was (sec) 1.080000 now iterating at: 11:50:52 rms-change max change #iterations 5.191034 252.3888 at 10iterations 2.655083 90.77817 at 20iterations 1.361339 42.83691 at 30iterations 0.6951968 19.77116 at 40iterations 0.3563691 9.958813 at 50iterations 0.1838928 5.410664 at 60iterations 9.3947992E-02 2.712498 at 70iterations 4.8282210E-02 1.274175 at 80iterations 2.4738465E-02 0.7519989 at 90iterations 1.2710819E-02 0.3771124 at 100iterations 6.5173479E-03 0.1783290 at 110iterations 3.3423426E-03 9.2074871E-02 at 120iterations finished qdiffx linear iterations at : 11:51:00 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 3.3423426E-03 9.2074871E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 11:51:01 9.673u 0.284s 0:10.41 95.5% 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 11:51:01 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: GLU 223 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.369581 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): -21.82700 24.42400 ymin,ymax (A): 9.141000 53.89600 zmin,zma (A): 5.166000 52.70900 x,y,z range (A): 46.25100 44.75500 47.54300 scale (grids/A): 3.369581 object centre (A): 1.298500 31.51850 28.93750 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.999990 assigned positive charge : 316.0119 centred at (gu) : 86.65888 88.06767 89.18502 assigned negative charge : -322.0120 centred at (gu) : 86.56158 87.71346 88.55585 start vw surface at 0.1400000 fill in re-entrant regions at 1.130000 boundary points on vw surface= 194363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18764 grid for indexing accessible points = 1.400000 m= 103493 mr = 140351 m= 44940 mr = 85465 m= 14607 mr = 37113 m= 3269 mr = 11704 m= 438 mr = 2419 m= 35 mr = 284 m= 0 mr = 18 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 2803 time to turn everything in is 2.550000 number of dielectric boundary points 83791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.690000 number of grid points assigned charge 15752 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) : 2.246387 object centre at (A) : 1.298500 31.51850 28.93750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.340638 0.1925119 midg,1,midg; midg,igrid,midg -0.2081683 -0.2638566 1,midg,midg; igrid,midg,midg -3.2080238E-04 -4.6086520E-02 gauss-seidel spectral radius is 0.9993250 estimated iterations to convergence 304 setup time was (sec) 2.870000 now iterating at: 11:51:04 rms-change max change #iterations 11.25249 328.9872 at 10iterations 6.667729 128.8613 at 20iterations 3.948967 86.46294 at 30iterations 2.332169 42.61064 at 40iterations 1.377224 23.32383 at 50iterations 0.8120245 13.46326 at 60iterations 0.4778153 7.204981 at 70iterations 0.2822826 4.478903 at 80iterations 0.1661227 2.664531 at 90iterations 9.7841308E-02 1.777342 at 100iterations 5.7709280E-02 0.8637857 at 110iterations 3.3937905E-02 0.5411825 at 120iterations 1.9989377E-02 0.3136927 at 130iterations 1.1748012E-02 0.2065582 at 140iterations 6.9454466E-03 0.1139827 at 150iterations 4.0778727E-03 7.1475446E-02 at 160iterations 2.4022791E-03 4.1334152E-02 at 170iterations 1.4150821E-03 2.3497581E-02 at 180iterations finished qdiffx linear iterations at : 11:51:18 total time elapsed so far: 16.85000 # loops : 180 mean,max change (kT/e) : 1.4150821E-03 2.3497581E-02 energy calculations done at 16.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.03000 DelPhi exited at 11:51:19 17.029u 0.316s 0:18.03 96.1% 0+0k 0+0io 0pf+0w