Mon Oct 10 14:11:48 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 Mon Oct 10 2011 at 14:11:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6276667 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): -11.98000 43.52500 ymin,ymax (A): -10.64700 46.07100 zmin,zma (A): -27.86500 20.00600 x,y,z range (A): 55.50500 56.71800 47.87100 scale (grids/A): 0.6276667 object centre (A): 15.77250 17.71200 -3.929500 number of atom coordinates read : 2558 total number of charged atoms : 2384 net assigned charge : 3.500013 assigned positive charge : 378.9829 centred at (gu) : 89.41205 90.03791 91.15260 assigned negative charge : -375.4835 centred at (gu) : 89.43162 90.07668 91.10119 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7014 nv = 96 ne = 84 npr = 50310 no. pairs analyzed = 50310 no. exposed pairs = 3380 no. arc points = 24842 no. surface atoms = 1125 nbur = 1433 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 3644 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2430 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6830539E-10 9.7421191E-09 midg,1,midg; midg,igrid,midg 6.5212249E-09 3.7119893E-10 1,midg,midg; igrid,midg,midg 5.7271334E-09 1.7038410E-09 gauss-seidel spectral radius is 0.9868591 estimated iterations to convergence 71 setup time was (sec) 0.6900000 now iterating at: 14:11:49 rms-change max change #iterations 0.1305652 21.00620 at 10iterations 1.2039861E-02 1.789604 at 20iterations 1.1542991E-03 0.1701298 at 30iterations 1.0830509E-04 1.7176628E-02 at 40iterations 1.0550172E-05 1.5563965E-03 at 50iterations finished qdiffx linear iterations at : 14:11:53 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.0550172E-05 1.5563965E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 14:11:54 4.302u 0.221s 0:05.09 88.8% 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 Mon Oct 10 2011 at 14:11:54 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 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: 1.883000 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): -11.98000 43.52500 ymin,ymax (A): -10.64700 46.07100 zmin,zma (A): -27.86500 20.00600 x,y,z range (A): 55.50500 56.71800 47.87100 scale (grids/A): 1.883000 object centre (A): 15.77250 17.71200 -3.929500 number of atom coordinates read : 2558 total number of charged atoms : 2384 net assigned charge : 3.500013 assigned positive charge : 378.9829 centred at (gu) : 88.23581 90.11350 93.45734 assigned negative charge : -375.4835 centred at (gu) : 88.29456 90.22977 93.30339 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 74853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24842 grid for indexing accessible points = 1.400000 m= 27354 mr = 50512 m= 4401 mr = 19647 m= 254 mr = 2481 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 0.7400000 number of dielectric boundary points 34134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 18679 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) : 0.6276667 object centre at (A) : 15.77250 17.71200 -3.929500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0639304E-04 2.6089322E-02 midg,1,midg; midg,igrid,midg 1.0068823E-03 2.6305698E-02 1,midg,midg; igrid,midg,midg 1.0709316E-02 -6.1876867E-03 gauss-seidel spectral radius is 0.9986112 estimated iterations to convergence 213 setup time was (sec) 1.110000 now iterating at: 14:11:55 rms-change max change #iterations 4.128519 187.0912 at 10iterations 1.911283 72.37515 at 20iterations 0.8898922 30.43098 at 30iterations 0.4132375 13.33913 at 40iterations 0.1911178 6.381344 at 50iterations 8.8882178E-02 2.891197 at 60iterations 4.1372698E-02 1.395832 at 70iterations 1.9200342E-02 0.6370592 at 80iterations 8.9698248E-03 0.3058201 at 90iterations 4.1454285E-03 0.1359396 at 100iterations 1.9341564E-03 7.0058823E-02 at 110iterations 9.0191758E-04 2.8095245E-02 at 120iterations finished qdiffx linear iterations at : 14:12:03 total time elapsed so far: 8.950000 # loops : 120 mean,max change (kT/e) : 9.0191758E-04 2.8095245E-02 energy calculations done at 8.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.170000 DelPhi exited at 14:12:04 9.176u 0.249s 0:10.17 92.5% 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 14:12:04 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.824500 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): -11.98000 43.52500 ymin,ymax (A): -10.64700 46.07100 zmin,zma (A): -27.86500 20.00600 x,y,z range (A): 55.50500 56.71800 47.87100 scale (grids/A): 2.824500 object centre (A): 15.77250 17.71200 -3.929500 number of atom coordinates read : 2558 total number of charged atoms : 2384 net assigned charge : 3.500013 assigned positive charge : 378.9829 centred at (gu) : 87.35349 90.17007 95.18590 assigned negative charge : -375.4835 centred at (gu) : 87.44180 90.34465 94.95521 start vw surface at 0.1900000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 172626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24842 grid for indexing accessible points = 1.400000 m= 87762 mr = 122665 m= 32146 mr = 70514 m= 7746 mr = 25057 m= 1106 mr = 5482 m= 70 mr = 704 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 1.830000 number of dielectric boundary points 77018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 19070 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) : 1.883000 object centre at (A) : 15.77250 17.71200 -3.929500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8757711E-03 0.3300622 midg,1,midg; midg,igrid,midg 1.7135262E-02 0.4921298 1,midg,midg; igrid,midg,midg 0.1006346 1.8474035E-02 gauss-seidel spectral radius is 0.9992572 estimated iterations to convergence 290 setup time was (sec) 2.190000 now iterating at: 14:12:06 rms-change max change #iterations 9.751557 355.5566 at 10iterations 5.770681 161.8009 at 20iterations 3.370835 81.20842 at 30iterations 1.964306 46.77909 at 40iterations 1.141864 22.40508 at 50iterations 0.6608368 14.80686 at 60iterations 0.3820227 8.007385 at 70iterations 0.2203481 4.452723 at 80iterations 0.1270866 2.500114 at 90iterations 7.3133394E-02 1.395638 at 100iterations 4.2127069E-02 0.7520957 at 110iterations 2.4202479E-02 0.4548340 at 120iterations 1.3914994E-02 0.2427750 at 130iterations 7.9908706E-03 0.1642560 at 140iterations 4.5930878E-03 8.6149216E-02 at 150iterations 2.6320121E-03 5.3757191E-02 at 160iterations 1.5139177E-03 2.8442383E-02 at 170iterations 8.6901645E-04 1.5342712E-02 at 180iterations finished qdiffx linear iterations at : 14:12:18 total time elapsed so far: 14.30000 # loops : 180 mean,max change (kT/e) : 8.6901645E-04 1.5342712E-02 energy calculations done at 14.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.52000 DelPhi exited at 14:12:19 14.525u 0.253s 0:15.22 97.0% 0+0k 0+0io 0pf+0w