Sat Oct 8 17:01:31 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 Sat Oct 8 2011 at 17:01:31 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3419 !!! WARNING: ILE 375 has a net charge of -0.2720 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: 0.5289433 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): 35.77700 94.73700 ymin,ymax (A): 14.08700 81.39100 zmin,zma (A): -23.19500 25.11000 x,y,z range (A): 58.96000 67.30400 48.30500 scale (grids/A): 0.5289433 object centre (A): 65.25700 47.73900 0.9574995 number of atom coordinates read : 3419 total number of charged atoms : 3274 net assigned charge : -3.771990 assigned positive charge : 518.5522 centred at (gu) : 90.51217 90.27753 89.76521 assigned negative charge : -522.3257 centred at (gu) : 90.49372 90.30247 89.74885 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6118 nv = 96 ne = 84 npr = 70188 no. pairs analyzed = 70188 no. exposed pairs = 4190 no. arc points = 28907 no. surface atoms = 1414 nbur = 2005 mkacc time = 0.1800000 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 = 1.596000 m= 222 mr = 3262 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2965 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8173 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9567438E-10 -4.9200866E-11 midg,1,midg; midg,igrid,midg -1.6611365E-11 -2.3525351E-10 1,midg,midg; igrid,midg,midg -1.6959671E-10 -4.8960721E-11 gauss-seidel spectral radius is 0.9816136 estimated iterations to convergence 61 setup time was (sec) 0.6900000 now iterating at: 17:01:32 rms-change max change #iterations 6.9462046E-02 10.89515 at 10iterations 4.3017813E-03 0.7730942 at 20iterations 2.8600471E-04 4.7334671E-02 at 30iterations 3.0232033E-05 6.9642067E-03 at 40iterations 6.2311110E-06 1.6283989E-03 at 50iterations finished qdiffx linear iterations at : 17:01:35 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 6.2311110E-06 1.6283989E-03 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 17:01:36 4.337u 0.261s 0:04.87 94.2% 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 Sat Oct 8 2011 at 17:01:36 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3419 !!! WARNING: ILE 375 has a net charge of -0.2720 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: 1.586830 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): 35.77700 94.73700 ymin,ymax (A): 14.08700 81.39100 zmin,zma (A): -23.19500 25.11000 x,y,z range (A): 58.96000 67.30400 48.30500 scale (grids/A): 1.586830 object centre (A): 65.25700 47.73900 0.9574995 number of atom coordinates read : 3419 total number of charged atoms : 3274 net assigned charge : -3.771990 assigned positive charge : 518.5522 centred at (gu) : 91.53568 90.83195 89.29477 assigned negative charge : -522.3257 centred at (gu) : 91.48042 90.90701 89.24618 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28907 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21338 mr = 47520 m= 2148 mr = 14662 m= 65 mr = 1023 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.5100000 number of dielectric boundary points 28830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 387 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 24814 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) : 0.5289433 object centre at (A) : 65.25700 47.73900 0.9574995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6013823E-03 -2.7210345E-03 midg,1,midg; midg,igrid,midg 1.7949007E-02 1.3193447E-02 1,midg,midg; igrid,midg,midg -1.5143951E-02 -2.0899868E-03 gauss-seidel spectral radius is 0.9981123 estimated iterations to convergence 183 setup time was (sec) 0.8500000 now iterating at: 17:01:37 rms-change max change #iterations 3.416253 145.8616 at 10iterations 1.397744 59.29664 at 20iterations 0.5725778 21.52792 at 30iterations 0.2354762 8.389999 at 40iterations 9.6438400E-02 3.298469 at 50iterations 3.9611779E-02 1.582644 at 60iterations 1.6283993E-02 0.6294708 at 70iterations 6.6863988E-03 0.2420330 at 80iterations 2.7558077E-03 9.5527649E-02 at 90iterations 1.1368702E-03 4.3350220E-02 at 100iterations 4.6966804E-04 1.5698195E-02 at 110iterations 1.9762239E-04 7.7047348E-03 at 120iterations finished qdiffx linear iterations at : 17:01:45 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.9762239E-04 7.7047348E-03 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 17:01:46 9.618u 0.283s 0:10.19 97.0% 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 8 2011 at 17:01:46 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3419 !!! WARNING: ILE 375 has a net charge of -0.2720 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: 2.380245 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): 35.77700 94.73700 ymin,ymax (A): 14.08700 81.39100 zmin,zma (A): -23.19500 25.11000 x,y,z range (A): 58.96000 67.30400 48.30500 scale (grids/A): 2.380245 object centre (A): 65.25700 47.73900 0.9574995 number of atom coordinates read : 3419 total number of charged atoms : 3274 net assigned charge : -3.771990 assigned positive charge : 518.5522 centred at (gu) : 92.30338 91.24755 88.94189 assigned negative charge : -522.3257 centred at (gu) : 92.22053 91.36045 88.86919 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 159344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28907 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 74391 mr = 116192 m= 20553 mr = 59192 m= 3159 mr = 15190 m= 207 mr = 2029 m= 5 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 302 time to turn everything in is 1.300000 number of dielectric boundary points 64994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 26149 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) : 1.586830 object centre at (A) : 65.25700 47.73900 0.9574995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1157283E-02 -4.0204402E-02 midg,1,midg; midg,igrid,midg 0.4838469 0.4496506 1,midg,midg; igrid,midg,midg -0.2455748 -2.5465768E-03 gauss-seidel spectral radius is 0.9991194 estimated iterations to convergence 266 setup time was (sec) 1.670000 now iterating at: 17:01:48 rms-change max change #iterations 8.899376 283.3394 at 10iterations 4.949909 126.2987 at 20iterations 2.739745 59.61240 at 30iterations 1.504383 30.06020 at 40iterations 0.8283818 16.89317 at 50iterations 0.4543421 9.403715 at 60iterations 0.2492564 5.622971 at 70iterations 0.1361518 2.691107 at 80iterations 7.4522689E-02 1.558726 at 90iterations 4.0713854E-02 0.8496475 at 100iterations 2.2302404E-02 0.4957666 at 110iterations 1.2177506E-02 0.2535553 at 120iterations 6.6657206E-03 0.1356487 at 130iterations 3.6474254E-03 7.7583313E-02 at 140iterations 1.9936110E-03 3.8771629E-02 at 150iterations 1.0903417E-03 2.3551464E-02 at 160iterations 5.9897389E-04 1.2561798E-02 at 170iterations 3.3016177E-04 7.3844194E-03 at 180iterations finished qdiffx linear iterations at : 17:02:02 total time elapsed so far: 16.07000 # loops : 180 mean,max change (kT/e) : 3.3016177E-04 7.3844194E-03 energy calculations done at 16.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.26000 DelPhi exited at 17:02:03 16.258u 0.335s 0:16.88 98.2% 0+0k 0+0io 0pf+0w