Sun Oct 9 07:45:18 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 Sun Oct 9 2011 at 07:45:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 0.5488660 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): -3.957000 42.17500 ymin,ymax (A): 35.81600 89.04300 zmin,zma (A): -3.040000 61.82100 x,y,z range (A): 46.13200 53.22700 64.86100 scale (grids/A): 0.5488660 object centre (A): 19.10900 62.42950 29.39050 number of atom coordinates read : 2550 total number of charged atoms : 2403 net assigned charge : -12.49998 assigned positive charge : 379.9679 centred at (gu) : 90.41759 88.85988 89.67117 assigned negative charge : -392.4683 centred at (gu) : 90.57697 88.53156 89.63876 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5122 nv = 96 ne = 84 npr = 51058 no. pairs analyzed = 51058 no. exposed pairs = 3525 no. arc points = 25306 no. surface atoms = 1188 nbur = 1362 mkacc time = 0.1100000 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 = 1.540000 m= 197 mr = 2426 m= 0 mr = 12 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2511 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1299736E-09 -5.7558547E-10 midg,1,midg; midg,igrid,midg -4.0683950E-09 9.1187696E-10 1,midg,midg; igrid,midg,midg 1.6383622E-10 -2.0957527E-09 gauss-seidel spectral radius is 0.9828588 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 07:45:18 rms-change max change #iterations 6.7348413E-02 13.36613 at 10iterations 4.3663578E-03 0.7326698 at 20iterations 2.9552929E-04 5.9947968E-02 at 30iterations 2.0576361E-05 3.5190582E-03 at 40iterations 1.4707052E-06 2.7561188E-04 at 50iterations finished qdiffx linear iterations at : 07:45:21 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.4707052E-06 2.7561188E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 07:45:21 3.169u 0.159s 0:03.59 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 Sun Oct 9 2011 at 07:45:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 1.646598 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): -3.957000 42.17500 ymin,ymax (A): 35.81600 89.04300 zmin,zma (A): -3.040000 61.82100 x,y,z range (A): 46.13200 53.22700 64.86100 scale (grids/A): 1.646598 object centre (A): 19.10900 62.42950 29.39050 number of atom coordinates read : 2550 total number of charged atoms : 2403 net assigned charge : -12.49998 assigned positive charge : 379.9679 centred at (gu) : 91.25241 86.57903 89.01325 assigned negative charge : -392.4683 centred at (gu) : 91.73060 85.59448 88.91594 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 55974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25306 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16737 mr = 35772 m= 1584 mr = 11268 m= 35 mr = 686 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.4400000 number of dielectric boundary points 26600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 18439 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) : 0.5488660 object centre at (A) : 19.10900 62.42950 29.39050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6946330E-02 -6.4601963E-03 midg,1,midg; midg,igrid,midg -2.7027860E-02 3.9776531E-03 1,midg,midg; igrid,midg,midg -3.3410671E-03 -1.5189055E-02 gauss-seidel spectral radius is 0.9981717 estimated iterations to convergence 186 setup time was (sec) 0.7300000 now iterating at: 07:45:22 rms-change max change #iterations 3.109142 166.0996 at 10iterations 1.292185 54.57186 at 20iterations 0.5347582 23.87000 at 30iterations 0.2209753 8.477419 at 40iterations 9.1952845E-02 3.520304 at 50iterations 3.8198400E-02 1.470367 at 60iterations 1.5797652E-02 0.6189308 at 70iterations 6.5644588E-03 0.2802582 at 80iterations 2.7227616E-03 0.1032333 at 90iterations 1.1296613E-03 4.3236256E-02 at 100iterations 4.6938824E-04 1.8152237E-02 at 110iterations 1.9500584E-04 7.2466135E-03 at 120iterations finished qdiffx linear iterations at : 07:45:29 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 1.9500584E-04 7.2466135E-03 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 07:45:29 7.574u 0.214s 0:08.05 96.6% 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 Sun Oct 9 2011 at 07:45:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 2.469897 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): -3.957000 42.17500 ymin,ymax (A): 35.81600 89.04300 zmin,zma (A): -3.040000 61.82100 x,y,z range (A): 46.13200 53.22700 64.86100 scale (grids/A): 2.469897 object centre (A): 19.10900 62.42950 29.39050 number of atom coordinates read : 2550 total number of charged atoms : 2403 net assigned charge : -12.49998 assigned positive charge : 379.9679 centred at (gu) : 91.87847 84.86845 88.51964 assigned negative charge : -392.4683 centred at (gu) : 92.59576 83.39163 88.37377 start vw surface at 0.1400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 129663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25306 grid for indexing accessible points = 1.400000 m= 58586 mr = 87805 m= 15684 mr = 45769 m= 2263 mr = 11373 m= 147 mr = 1381 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 744 time to turn everything in is 0.9700000 number of dielectric boundary points 59954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 19197 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) : 1.646598 object centre at (A) : 19.10900 62.42950 29.39050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9683164 -0.1066037 midg,1,midg; midg,igrid,midg -0.3535654 7.7736117E-02 1,midg,midg; igrid,midg,midg -5.0708722E-02 -0.1949646 gauss-seidel spectral radius is 0.9991282 estimated iterations to convergence 268 setup time was (sec) 1.280000 now iterating at: 07:45:31 rms-change max change #iterations 8.166217 277.6918 at 10iterations 4.561447 159.1123 at 20iterations 2.552351 62.14997 at 30iterations 1.415501 39.71504 at 40iterations 0.7856658 19.97888 at 50iterations 0.4351606 9.412836 at 60iterations 0.2399475 5.399100 at 70iterations 0.1322608 3.265497 at 80iterations 7.2817333E-02 1.975456 at 90iterations 3.9970107E-02 0.9242229 at 100iterations 2.1952271E-02 0.5166095 at 110iterations 1.2057963E-02 0.2808933 at 120iterations 6.6081784E-03 0.1496973 at 130iterations 3.6164927E-03 8.2391381E-02 at 140iterations 1.9782614E-03 4.2821884E-02 at 150iterations 1.0862474E-03 2.8204441E-02 at 160iterations 5.9538905E-04 1.3231397E-02 at 170iterations 3.2572576E-04 8.0261230E-03 at 180iterations finished qdiffx linear iterations at : 07:45:41 total time elapsed so far: 11.75000 # loops : 180 mean,max change (kT/e) : 3.2572576E-04 8.0261230E-03 energy calculations done at 11.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 07:45:42 11.930u 0.228s 0:12.61 96.3% 0+0k 0+0io 0pf+0w