Sun Oct 9 00:20:16 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 00:20:17 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 0.5746291 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): -15.94300 40.56900 ymin,ymax (A): 16.47800 76.41200 zmin,zma (A): 25.55700 87.51000 x,y,z range (A): 56.51200 59.93401 61.95300 scale (grids/A): 0.5746291 object centre (A): 12.31300 46.44500 56.53350 number of atom coordinates read : 3254 total number of charged atoms : 3113 net assigned charge : 12.95702 assigned positive charge : 477.5658 centred at (gu) : 89.82384 90.03987 90.64288 assigned negative charge : -464.6104 centred at (gu) : 89.68068 90.06489 90.83717 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7402 nv = 96 ne = 84 npr = 63633 no. pairs analyzed = 63633 no. exposed pairs = 4240 no. arc points = 30878 no. surface atoms = 1415 nbur = 1839 mkacc time = 0.1400000 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 = 1.484000 m= 327 mr = 3809 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3146 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9347 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1876592E-09 -1.7031925E-09 midg,1,midg; midg,igrid,midg 2.8371245E-09 1.9187536E-09 1,midg,midg; igrid,midg,midg -4.3946696E-10 4.8831201E-09 gauss-seidel spectral radius is 0.9844083 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 00:20:17 rms-change max change #iterations 9.7894341E-02 18.96236 at 10iterations 7.4438490E-03 1.254772 at 20iterations 5.8914616E-04 8.3299637E-02 at 30iterations 5.4393058E-05 8.0037117E-03 at 40iterations 6.8659324E-06 7.6293945E-04 at 50iterations finished qdiffx linear iterations at : 00:20:20 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 6.8659324E-06 7.6293945E-04 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 00:20:20 3.218u 0.153s 0:03.70 90.8% 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 Sun Oct 9 2011 at 00:20:20 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 1.723887 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): -15.94300 40.56900 ymin,ymax (A): 16.47800 76.41200 zmin,zma (A): 25.55700 87.51000 x,y,z range (A): 56.51200 59.93401 61.95300 scale (grids/A): 1.723887 object centre (A): 12.31300 46.44500 56.53350 number of atom coordinates read : 3254 total number of charged atoms : 3113 net assigned charge : 12.95702 assigned positive charge : 477.5658 centred at (gu) : 89.47044 90.11890 91.92777 assigned negative charge : -464.6104 centred at (gu) : 89.04192 90.19433 92.51123 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30878 grid for indexing accessible points = 1.400000 m= 26323 mr = 54655 m= 3229 mr = 18188 m= 119 mr = 1638 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 758 time to turn everything in is 0.5400000 number of dielectric boundary points 36293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 24151 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) : 0.5746291 object centre at (A) : 12.31300 46.44500 56.53350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9887944E-02 7.3815389E-03 midg,1,midg; midg,igrid,midg 3.7158832E-02 1.7504685E-02 1,midg,midg; igrid,midg,midg -9.1889473E-03 1.5289049E-02 gauss-seidel spectral radius is 0.9984252 estimated iterations to convergence 200 setup time was (sec) 0.8200000 now iterating at: 00:20:21 rms-change max change #iterations 3.852036 148.2250 at 10iterations 1.694371 61.10360 at 20iterations 0.7496251 24.99909 at 30iterations 0.3307096 10.66566 at 40iterations 0.1462317 4.872759 at 50iterations 6.4760163E-02 2.132081 at 60iterations 2.8703993E-02 0.8895760 at 70iterations 1.2707074E-02 0.4677124 at 80iterations 5.6056660E-03 0.1923599 at 90iterations 2.4813861E-03 9.7099006E-02 at 100iterations 1.1020495E-03 3.5486221E-02 at 110iterations 4.8771076E-04 1.4913082E-02 at 120iterations finished qdiffx linear iterations at : 00:20:27 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 4.8771076E-04 1.4913082E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 00:20:28 7.183u 0.217s 0:07.69 96.0% 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 Sun Oct 9 2011 at 00:20:28 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.585831 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): -15.94300 40.56900 ymin,ymax (A): 16.47800 76.41200 zmin,zma (A): 25.55700 87.51000 x,y,z range (A): 56.51200 59.93401 61.95300 scale (grids/A): 2.585831 object centre (A): 12.31300 46.44500 56.53350 number of atom coordinates read : 3254 total number of charged atoms : 3113 net assigned charge : 12.95702 assigned positive charge : 477.5658 centred at (gu) : 89.20525 90.17795 92.89128 assigned negative charge : -464.6104 centred at (gu) : 88.56298 90.29137 93.76680 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 188446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30878 grid for indexing accessible points = 1.400000 m= 88718 mr = 133842 m= 27604 mr = 70159 m= 5349 mr = 21014 m= 537 mr = 3583 m= 14 mr = 280 m= 0 mr = 2 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 2480 time to turn everything in is 1.320000 number of dielectric boundary points 81788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 24873 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) : 1.723887 object centre at (A) : 12.31300 46.44500 56.53350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7354300 9.5469303E-02 midg,1,midg; midg,igrid,midg 0.6121817 0.3469158 1,midg,midg; igrid,midg,midg -7.1886227E-02 0.2188871 gauss-seidel spectral radius is 0.9992265 estimated iterations to convergence 284 setup time was (sec) 1.600000 now iterating at: 00:20:30 rms-change max change #iterations 9.760319 291.4797 at 10iterations 5.688534 128.4525 at 20iterations 3.296608 73.81021 at 30iterations 1.898346 46.30145 at 40iterations 1.087254 24.22073 at 50iterations 0.6231443 13.55020 at 60iterations 0.3553793 7.183182 at 70iterations 0.2028289 4.353113 at 80iterations 0.1154943 2.141678 at 90iterations 6.5710083E-02 1.336727 at 100iterations 3.7380468E-02 0.7018065 at 110iterations 2.1172540E-02 0.3600340 at 120iterations 1.2038151E-02 0.2186031 at 130iterations 6.8358663E-03 0.1219693 at 140iterations 3.8770004E-03 6.8511963E-02 at 150iterations 2.2014789E-03 4.4122696E-02 at 160iterations 1.2492068E-03 2.4398804E-02 at 170iterations 7.0864108E-04 1.2807846E-02 at 180iterations finished qdiffx linear iterations at : 00:20:40 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 7.0864108E-04 1.2807846E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 00:20:40 11.605u 0.237s 0:12.11 97.6% 0+0k 0+0io 0pf+0w