Sun Oct 9 12:34:52 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 Sun Oct 9 2011 at 12:34:52 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2395 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: 0.6898823 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): -7.000000 44.26300 ymin,ymax (A): -13.99300 37.61000 zmin,zma (A): 1.705000 44.33700 x,y,z range (A): 51.26300 51.60300 42.63200 scale (grids/A): 0.6898823 object centre (A): 18.63150 11.80850 23.02100 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 3.500025 assigned positive charge : 368.5011 centred at (gu) : 89.88492 91.08488 91.00859 assigned negative charge : -365.0015 centred at (gu) : 89.86463 91.26614 91.08689 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7742 nv = 96 ne = 84 npr = 47857 no. pairs analyzed = 47857 no. exposed pairs = 2946 no. arc points = 20384 no. surface atoms = 998 nbur = 1397 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 501 mr = 4429 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1888 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8681 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1377525E-08 -1.2502047E-08 midg,1,midg; midg,igrid,midg 7.1838585E-08 -6.3770422E-08 1,midg,midg; igrid,midg,midg 1.2976826E-08 2.7735203E-08 gauss-seidel spectral radius is 0.9890853 estimated iterations to convergence 78 setup time was (sec) 0.4700000 now iterating at: 12:34:53 rms-change max change #iterations 0.1977274 34.09554 at 10iterations 2.4227776E-02 3.118569 at 20iterations 3.4776400E-03 0.4831963 at 30iterations 8.2826731E-04 0.1137695 at 40iterations 2.8214944E-04 3.9432526E-02 at 50iterations finished qdiffx linear iterations at : 12:34:55 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 2.8214944E-04 3.9432526E-02 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 12:34:56 3.038u 0.147s 0:03.45 91.8% 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 12:34:56 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.069647 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): -7.000000 44.26300 ymin,ymax (A): -13.99300 37.61000 zmin,zma (A): 1.705000 44.33700 x,y,z range (A): 51.26300 51.60300 42.63200 scale (grids/A): 2.069647 object centre (A): 18.63150 11.80850 23.02100 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 3.500025 assigned positive charge : 368.5011 centred at (gu) : 89.65418 93.25430 93.02502 assigned negative charge : -365.0015 centred at (gu) : 89.59344 93.79813 93.26040 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20384 grid for indexing accessible points = 1.400000 m= 32954 mr = 58176 m= 6017 mr = 24841 m= 566 mr = 3960 m= 12 mr = 313 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 34628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17865 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) : 0.6898823 object centre at (A) : 18.63150 11.80850 23.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4505620E-02 1.2143865E-03 midg,1,midg; midg,igrid,midg 1.5290431E-02 -6.8886794E-02 1,midg,midg; igrid,midg,midg 4.6415519E-02 3.8380423E-03 gauss-seidel spectral radius is 0.9988152 estimated iterations to convergence 230 setup time was (sec) 0.8400000 now iterating at: 12:34:57 rms-change max change #iterations 4.893389 261.8706 at 10iterations 2.403923 81.02950 at 20iterations 1.190158 34.19284 at 30iterations 0.5870215 18.96372 at 40iterations 0.2918926 8.921365 at 50iterations 0.1439807 4.316990 at 60iterations 7.1119294E-02 2.645050 at 70iterations 3.5464324E-02 1.070618 at 80iterations 1.7712306E-02 0.5331974 at 90iterations 8.9446073E-03 0.2520218 at 100iterations 4.6410100E-03 0.1319237 at 110iterations 2.5063802E-03 7.6632500E-02 at 120iterations finished qdiffx linear iterations at : 12:35:02 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 2.5063802E-03 7.6632500E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 12:35:03 6.890u 0.156s 0:07.32 96.1% 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 12:35:03 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.104471 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): -7.000000 44.26300 ymin,ymax (A): -13.99300 37.61000 zmin,zma (A): 1.705000 44.33700 x,y,z range (A): 51.26300 51.60300 42.63200 scale (grids/A): 3.104471 object centre (A): 18.63150 11.80850 23.02100 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 3.500025 assigned positive charge : 368.5011 centred at (gu) : 89.48117 94.88118 94.53751 assigned negative charge : -365.0015 centred at (gu) : 89.39018 95.69718 94.89053 start vw surface at 0.1400000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 189754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20384 grid for indexing accessible points = 1.400000 m= 102759 mr = 139791 m= 41039 mr = 85391 m= 11412 mr = 33668 m= 2302 mr = 8811 m= 271 mr = 1697 m= 4 mr = 178 m= 0 mr = 2 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 78003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 18024 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) : 2.069647 object centre at (A) : 18.63150 11.80850 23.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5404998 -0.1188134 midg,1,midg; midg,igrid,midg 0.3323351 -0.7417206 1,midg,midg; igrid,midg,midg 0.4872563 -0.2432211 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 2.090000 now iterating at: 12:35:05 rms-change max change #iterations 10.96742 407.0175 at 10iterations 6.498570 143.2720 at 20iterations 3.846810 80.70126 at 30iterations 2.260608 40.88215 at 40iterations 1.333185 25.10704 at 50iterations 0.7817595 13.86580 at 60iterations 0.4598271 7.426313 at 70iterations 0.2695740 5.035048 at 80iterations 0.1582820 2.873079 at 90iterations 9.2824437E-02 1.826038 at 100iterations 5.4362256E-02 0.9449520 at 110iterations 3.1997766E-02 0.5471277 at 120iterations 1.9092010E-02 0.3234329 at 130iterations 1.1555518E-02 0.2259216 at 140iterations 7.2022299E-03 0.1376801 at 150iterations 4.6920991E-03 9.7129822E-02 at 160iterations 3.2490843E-03 7.0598602E-02 at 170iterations 2.3883656E-03 5.0613403E-02 at 180iterations finished qdiffx linear iterations at : 12:35:15 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 2.3883656E-03 5.0613403E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 12:35:15 11.871u 0.172s 0:12.31 97.8% 0+0k 0+0io 0pf+0w