Mon Oct 10 14:03:55 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 14:03:55 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3284 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5952480 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): -1.668000 58.13900 ymin,ymax (A): -24.84800 27.13900 zmin,zma (A): -9.697001 45.56600 x,y,z range (A): 59.80700 51.98700 55.26300 scale (grids/A): 0.5952480 object centre (A): 28.23550 1.145500 17.93450 number of atom coordinates read : 3284 total number of charged atoms : 3137 net assigned charge : 2.500005 assigned positive charge : 491.3467 centred at (gu) : 91.61987 89.13270 90.27927 assigned negative charge : -488.8482 centred at (gu) : 91.68398 89.15075 90.25667 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7601 nv = 96 ne = 84 npr = 67945 no. pairs analyzed = 67945 no. exposed pairs = 3847 no. arc points = 26614 no. surface atoms = 1298 nbur = 1986 mkacc time = 0.1500000 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 = 1.456000 m= 347 mr = 4281 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3700000 number of dielectric boundary points 3640 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2644 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9593 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4694905E-11 1.9605275E-09 midg,1,midg; midg,igrid,midg 2.0234898E-09 2.0057549E-10 1,midg,midg; igrid,midg,midg 2.3948405E-09 -2.3685769E-09 gauss-seidel spectral radius is 0.9854470 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 14:03:56 rms-change max change #iterations 0.1180475 16.20057 at 10iterations 9.9902162E-03 1.698072 at 20iterations 8.6618098E-04 0.1281929 at 30iterations 9.2428185E-05 1.2363434E-02 at 40iterations 1.4580923E-05 2.3293495E-03 at 50iterations finished qdiffx linear iterations at : 14:03:58 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.4580923E-05 2.3293495E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 14:03:59 3.256u 0.156s 0:03.94 86.2% 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 Mon Oct 10 2011 at 14:03:59 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3284 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: 1.785744 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): -1.668000 58.13900 ymin,ymax (A): -24.84800 27.13900 zmin,zma (A): -9.697001 45.56600 x,y,z range (A): 59.80700 51.98700 55.26300 scale (grids/A): 1.785744 object centre (A): 28.23550 1.145500 17.93450 number of atom coordinates read : 3284 total number of charged atoms : 3137 net assigned charge : 2.500005 assigned positive charge : 491.3467 centred at (gu) : 94.85889 87.39697 90.83690 assigned negative charge : -488.8482 centred at (gu) : 95.05160 87.45206 90.76993 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 grid for indexing accessible points = 1.400000 m= 28332 mr = 59366 m= 3536 mr = 20530 m= 128 mr = 2023 m= 0 mr = 27 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2197 time to turn everything in is 0.5700000 number of dielectric boundary points 33726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 24418 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) : 0.5952480 object centre at (A) : 28.23550 1.145500 17.93450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1271024E-03 -2.2919428E-02 midg,1,midg; midg,igrid,midg 9.6180299E-03 8.3653191E-03 1,midg,midg; igrid,midg,midg 2.5775550E-02 9.0653747E-03 gauss-seidel spectral radius is 0.9985156 estimated iterations to convergence 206 setup time was (sec) 0.8400000 now iterating at: 14:04:00 rms-change max change #iterations 4.259601 200.8960 at 10iterations 1.928025 61.35792 at 20iterations 0.8715566 28.62863 at 30iterations 0.3960062 12.23254 at 40iterations 0.1794225 5.753790 at 50iterations 8.1729293E-02 2.457020 at 60iterations 3.7046820E-02 1.162178 at 70iterations 1.6822370E-02 0.5196457 at 80iterations 7.6771872E-03 0.2501678 at 90iterations 3.4767231E-03 0.1023483 at 100iterations 1.5851657E-03 4.7342300E-02 at 110iterations 7.2183774E-04 2.3951054E-02 at 120iterations finished qdiffx linear iterations at : 14:04:07 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 7.2183774E-04 2.3951054E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 14:04:08 8.221u 0.219s 0:08.81 95.6% 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 Mon Oct 10 2011 at 14:04:08 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3284 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: 2.678616 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): -1.668000 58.13900 ymin,ymax (A): -24.84800 27.13900 zmin,zma (A): -9.697001 45.56600 x,y,z range (A): 59.80700 51.98700 55.26300 scale (grids/A): 2.678616 object centre (A): 28.23550 1.145500 17.93450 number of atom coordinates read : 3284 total number of charged atoms : 3137 net assigned charge : 2.500005 assigned positive charge : 491.3467 centred at (gu) : 97.28812 86.09536 91.25519 assigned negative charge : -488.8482 centred at (gu) : 97.57738 86.17792 91.15468 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 194072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 grid for indexing accessible points = 1.400000 m= 95244 mr = 144012 m= 30481 mr = 77682 m= 5867 mr = 23959 m= 520 mr = 4145 m= 19 mr = 319 m= 0 mr = 6 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 7414 time to turn everything in is 1.490000 number of dielectric boundary points 76080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 25087 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) : 1.785744 object centre at (A) : 28.23550 1.145500 17.93450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6637528E-02 -0.3359613 midg,1,midg; midg,igrid,midg 4.5126915E-02 0.1098789 1,midg,midg; igrid,midg,midg 0.3145567 0.2047882 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 1.820000 now iterating at: 14:04:10 rms-change max change #iterations 10.25791 293.7068 at 10iterations 5.952772 139.9165 at 20iterations 3.423558 67.42495 at 30iterations 1.972042 36.48674 at 40iterations 1.128581 22.51241 at 50iterations 0.6447629 12.16591 at 60iterations 0.3689190 6.573558 at 70iterations 0.2106037 3.822079 at 80iterations 0.1201172 2.119701 at 90iterations 6.8446539E-02 1.248522 at 100iterations 3.9065212E-02 0.6757526 at 110iterations 2.2304911E-02 0.3956299 at 120iterations 1.2725827E-02 0.2200918 at 130iterations 7.2549679E-03 0.1321678 at 140iterations 4.1317455E-03 7.1792603E-02 at 150iterations 2.3666876E-03 4.2308807E-02 at 160iterations 1.3521787E-03 2.3357391E-02 at 170iterations 7.7569921E-04 1.5071869E-02 at 180iterations finished qdiffx linear iterations at : 14:04:22 total time elapsed so far: 14.08000 # loops : 180 mean,max change (kT/e) : 7.7569921E-04 1.5071869E-02 energy calculations done at 14.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.26000 DelPhi exited at 14:04:23 14.261u 0.250s 0:15.29 94.8% 0+0k 0+0io 0pf+0w