Sat Oct 15 12:49:37 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 Sat Oct 15 2011 at 12:49:37 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 = 2697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5215124 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): 76.90200 126.2690 ymin,ymax (A): -19.54800 48.71500 zmin,zma (A): 64.35900 114.4860 x,y,z range (A): 49.36700 68.26300 50.12700 scale (grids/A): 0.5215124 object centre (A): 101.5855 14.58350 89.42250 number of atom coordinates read : 2697 total number of charged atoms : 2555 net assigned charge : 1.000024 assigned positive charge : 389.3814 centred at (gu) : 90.53809 93.40001 91.44673 assigned negative charge : -388.3828 centred at (gu) : 90.50717 93.36268 91.54220 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4844 nv = 96 ne = 84 npr = 53004 no. pairs analyzed = 53004 no. exposed pairs = 3726 no. arc points = 26614 no. surface atoms = 1237 nbur = 1460 mkacc time = 9.0000004E-02 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 = 1.624000 m= 188 mr = 2286 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2491 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5706593E-10 -2.7750391E-10 midg,1,midg; midg,igrid,midg -2.4467211E-11 2.5536151E-10 1,midg,midg; igrid,midg,midg -3.9327812E-11 1.0318622E-10 gauss-seidel spectral radius is 0.9810534 estimated iterations to convergence 60 setup time was (sec) 0.4200000 now iterating at: 12:49:38 rms-change max change #iterations 5.4896466E-02 9.951559 at 10iterations 3.2233759E-03 0.6178818 at 20iterations 1.9659505E-04 3.8211823E-02 at 30iterations 1.5116041E-05 3.7689209E-03 at 40iterations 2.1042774E-06 5.3107738E-04 at 50iterations finished qdiffx linear iterations at : 12:49:41 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 2.1042774E-06 5.3107738E-04 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 12:49:42 3.680u 0.242s 0:04.86 80.6% 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 Sat Oct 15 2011 at 12:49:42 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 = 2697 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: 1.564537 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): 76.90200 126.2690 ymin,ymax (A): -19.54800 48.71500 zmin,zma (A): 64.35900 114.4860 x,y,z range (A): 49.36700 68.26300 50.12700 scale (grids/A): 1.564537 object centre (A): 101.5855 14.58350 89.42250 number of atom coordinates read : 2697 total number of charged atoms : 2555 net assigned charge : 1.000024 assigned positive charge : 389.3814 centred at (gu) : 91.61353 100.1994 94.33957 assigned negative charge : -388.3828 centred at (gu) : 91.52140 100.0881 94.62658 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 53273 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 15332 mr = 33809 m= 1570 mr = 10155 m= 34 mr = 755 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 509 time to turn everything in is 0.2800000 number of dielectric boundary points 25490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 19369 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) : 0.5215124 object centre at (A) : 101.5855 14.58350 89.42250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0245245E-03 1.5811339E-03 midg,1,midg; midg,igrid,midg -3.5346053E-03 -4.2867046E-03 1,midg,midg; igrid,midg,midg -6.1481370E-04 6.2605604E-03 gauss-seidel spectral radius is 0.9979942 estimated iterations to convergence 178 setup time was (sec) 0.5100000 now iterating at: 12:49:43 rms-change max change #iterations 2.785517 196.3717 at 10iterations 1.106026 48.93954 at 20iterations 0.4379706 18.28955 at 30iterations 0.1741908 6.857465 at 40iterations 6.9131702E-02 3.017399 at 50iterations 2.7677273E-02 1.108352 at 60iterations 1.0999108E-02 0.4212685 at 70iterations 4.3939627E-03 0.1752562 at 80iterations 1.7536920E-03 7.3503494E-02 at 90iterations 7.0064154E-04 2.8156996E-02 at 100iterations 2.8064245E-04 1.3105392E-02 at 110iterations 1.1238950E-04 4.7588348E-03 at 120iterations finished qdiffx linear iterations at : 12:49:51 total time elapsed so far: 8.780000 # loops : 120 mean,max change (kT/e) : 1.1238950E-04 4.7588348E-03 energy calculations done at 8.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.910000 DelPhi exited at 12:49:52 8.913u 0.234s 0:09.85 92.7% 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 Sat Oct 15 2011 at 12:49:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 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: 2.346806 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): 76.90200 126.2690 ymin,ymax (A): -19.54800 48.71500 zmin,zma (A): 64.35900 114.4860 x,y,z range (A): 49.36700 68.26300 50.12700 scale (grids/A): 2.346806 object centre (A): 101.5855 14.58350 89.42250 number of atom coordinates read : 2697 total number of charged atoms : 2555 net assigned charge : 1.000024 assigned positive charge : 389.3814 centred at (gu) : 92.42000 105.2988 96.50913 assigned negative charge : -388.3828 centred at (gu) : 92.28207 105.1320 96.93986 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 124091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 52814 mr = 83842 m= 15234 mr = 40319 m= 2398 mr = 11299 m= 107 mr = 1525 m= 0 mr = 24 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1557 time to turn everything in is 0.6700000 number of dielectric boundary points 57635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20406 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) : 1.564537 object centre at (A) : 101.5855 14.58350 89.42250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5938645E-02 4.0842552E-02 midg,1,midg; midg,igrid,midg -2.5993858E-02 -5.7667267E-02 1,midg,midg; igrid,midg,midg -5.3289519E-03 0.1111602 gauss-seidel spectral radius is 0.9990730 estimated iterations to convergence 260 setup time was (sec) 0.9100000 now iterating at: 12:49:53 rms-change max change #iterations 7.437900 286.3741 at 10iterations 4.076519 124.1152 at 20iterations 2.217136 65.77251 at 30iterations 1.202036 32.26429 at 40iterations 0.6505855 15.75636 at 50iterations 0.3506332 8.653955 at 60iterations 0.1888818 4.688002 at 70iterations 0.1017572 2.503044 at 80iterations 5.4608226E-02 1.207140 at 90iterations 2.9306713E-02 0.6872864 at 100iterations 1.5764480E-02 0.3687325 at 110iterations 8.4342789E-03 0.2232161 at 120iterations 4.5456286E-03 0.1043167 at 130iterations 2.4351568E-03 5.5390358E-02 at 140iterations 1.3061386E-03 2.9152870E-02 at 150iterations 6.9829088E-04 1.7309189E-02 at 160iterations 3.7599236E-04 8.7242126E-03 at 170iterations 2.0135345E-04 4.7733486E-03 at 180iterations finished qdiffx linear iterations at : 12:50:06 total time elapsed so far: 13.74000 # loops : 180 mean,max change (kT/e) : 2.0135345E-04 4.7733486E-03 energy calculations done at 13.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 12:50:07 13.882u 0.268s 0:15.11 93.5% 0+0k 0+0io 0pf+0w