Tue Oct 11 03:25:10 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 Tue Oct 11 2011 at 03:25:10 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1168 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7481349 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): -6.973000 30.44200 ymin,ymax (A): 1.162000 40.11400 zmin,zma (A): -1.101000 46.48400 x,y,z range (A): 37.41500 38.95200 47.58500 scale (grids/A): 0.7481349 object centre (A): 11.73450 20.63800 22.69150 number of atom coordinates read : 1168 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 89.27029 89.10943 88.35091 assigned negative charge : -169.8232 centred at (gu) : 88.96349 89.08039 88.38339 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4431 nv = 96 ne = 84 npr = 22628 no. pairs analyzed = 22628 no. exposed pairs = 1486 no. arc points = 11029 no. surface atoms = 501 nbur = 667 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 2287 m= 0 mr = 54 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.1200000 number of dielectric boundary points 2378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 888 ## 84 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8523707E-07 7.2110666E-08 midg,1,midg; midg,igrid,midg 1.1510360E-07 1.1513612E-07 1,midg,midg; igrid,midg,midg -9.6753922E-08 2.6675778E-07 gauss-seidel spectral radius is 0.9905909 estimated iterations to convergence 84 setup time was (sec) 0.2900000 now iterating at: 03:25:11 rms-change max change #iterations 0.1855592 37.59972 at 10iterations 2.5571572E-02 3.858269 at 20iterations 3.4428788E-03 0.6876774 at 30iterations 4.6492793E-04 9.2458725E-02 at 40iterations 6.2553940E-05 1.1596680E-02 at 50iterations finished qdiffx linear iterations at : 03:25:14 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 6.2553940E-05 1.1596680E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 03:25:14 3.270u 0.170s 0:03.73 92.2% 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 Tue Oct 11 2011 at 03:25:14 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1168 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.244405 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): -6.973000 30.44200 ymin,ymax (A): 1.162000 40.11400 zmin,zma (A): -1.101000 46.48400 x,y,z range (A): 37.41500 38.95200 47.58500 scale (grids/A): 2.244405 object centre (A): 11.73450 20.63800 22.69150 number of atom coordinates read : 1168 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 87.81101 87.32843 85.05296 assigned negative charge : -169.8232 centred at (gu) : 86.89064 87.24122 85.15034 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 46107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11029 grid for indexing accessible points = 1.400000 m= 17640 mr = 30027 m= 3576 mr = 13317 m= 354 mr = 2448 m= 15 mr = 208 m= 0 mr = 8 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.2500000 number of dielectric boundary points 21684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8471 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) : 0.7481349 object centre at (A) : 11.73450 20.63800 22.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0674245E-02 9.6079614E-03 midg,1,midg; midg,igrid,midg 4.3455742E-02 3.4177519E-02 1,midg,midg; igrid,midg,midg -2.9341217E-02 4.2990040E-02 gauss-seidel spectral radius is 0.9988537 estimated iterations to convergence 234 setup time was (sec) 0.4600000 now iterating at: 03:25:15 rms-change max change #iterations 3.663820 202.6268 at 10iterations 1.822835 77.18486 at 20iterations 0.9090272 37.12288 at 30iterations 0.4513354 17.26966 at 40iterations 0.2263235 7.873028 at 50iterations 0.1122440 4.086969 at 60iterations 5.5810127E-02 2.138331 at 70iterations 2.7884251E-02 1.022942 at 80iterations 1.3842897E-02 0.5022774 at 90iterations 6.8891621E-03 0.2587743 at 100iterations 3.4232372E-03 0.1248484 at 110iterations 1.7009458E-03 6.1561584E-02 at 120iterations finished qdiffx linear iterations at : 03:25:22 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 1.7009458E-03 6.1561584E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 03:25:22 7.625u 0.238s 0:08.19 95.8% 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 Tue Oct 11 2011 at 03:25:22 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1168 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.366607 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): -6.973000 30.44200 ymin,ymax (A): 1.162000 40.11400 zmin,zma (A): -1.101000 46.48400 x,y,z range (A): 37.41500 38.95200 47.58500 scale (grids/A): 3.366607 object centre (A): 11.73450 20.63800 22.69150 number of atom coordinates read : 1168 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 86.71661 85.99263 82.57948 assigned negative charge : -169.8232 centred at (gu) : 85.33597 85.86192 82.72553 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 106156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11029 grid for indexing accessible points = 1.400000 m= 53885 mr = 72735 m= 22768 mr = 44086 m= 6773 mr = 18888 m= 1391 mr = 5299 m= 226 mr = 1127 m= 26 mr = 168 m= 0 mr = 21 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 432 time to turn everything in is 0.7300000 number of dielectric boundary points 48901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 8488 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) : 2.244405 object centre at (A) : 11.73450 20.63800 22.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3727360 7.5747885E-02 midg,1,midg; midg,igrid,midg 0.4013948 0.2876885 1,midg,midg; igrid,midg,midg -0.2365372 0.3003750 gauss-seidel spectral radius is 0.9992958 estimated iterations to convergence 297 setup time was (sec) 0.9500000 now iterating at: 03:25:23 rms-change max change #iterations 7.926310 378.1302 at 10iterations 4.611297 120.1651 at 20iterations 2.676983 60.30235 at 30iterations 1.553793 32.45042 at 40iterations 0.9042063 20.10737 at 50iterations 0.5234705 10.70089 at 60iterations 0.3036041 6.756535 at 70iterations 0.1763762 3.829024 at 80iterations 0.1023173 2.184995 at 90iterations 5.9476260E-02 1.226501 at 100iterations 3.4472577E-02 0.7525101 at 110iterations 2.0012880E-02 0.4286397 at 120iterations 1.1572543E-02 0.2524567 at 130iterations 6.7292363E-03 0.1359482 at 140iterations 3.9082612E-03 7.5988770E-02 at 150iterations 2.2734865E-03 4.9926758E-02 at 160iterations 1.3163206E-03 2.9720962E-02 at 170iterations 7.6543819E-04 1.5941620E-02 at 180iterations finished qdiffx linear iterations at : 03:25:34 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 7.6543819E-04 1.5941620E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.83000 DelPhi exited at 03:25:35 11.831u 0.209s 0:12.37 97.2% 0+0k 0+0io 0pf+0w