Sat Oct 8 11:35:05 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 8 2011 at 11:35:05 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 = 2559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5379919 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): -10.51700 33.40000 ymin,ymax (A): -38.65000 27.52200 zmin,zma (A): -14.42900 38.99200 x,y,z range (A): 43.91700 66.17200 53.42100 scale (grids/A): 0.5379919 object centre (A): 11.44150 -5.564000 12.28150 number of atom coordinates read : 2559 total number of charged atoms : 2410 net assigned charge : -1.499990 assigned positive charge : 373.1237 centred at (gu) : 90.72314 92.34846 91.51515 assigned negative charge : -374.6245 centred at (gu) : 90.73244 92.40018 91.53548 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4713 nv = 96 ne = 84 npr = 52299 no. pairs analyzed = 52299 no. exposed pairs = 3340 no. arc points = 23272 no. surface atoms = 1134 nbur = 1425 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 = 1.596000 m= 171 mr = 2338 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2349 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6251 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4844334E-11 -2.0992813E-10 midg,1,midg; midg,igrid,midg 8.2146498E-11 -4.9769849E-10 1,midg,midg; igrid,midg,midg -1.8785758E-11 -1.1725688E-10 gauss-seidel spectral radius is 0.9821602 estimated iterations to convergence 62 setup time was (sec) 0.5900000 now iterating at: 11:35:06 rms-change max change #iterations 6.1303791E-02 12.22603 at 10iterations 4.0285718E-03 0.5943832 at 20iterations 3.3758298E-04 7.3743820E-02 at 30iterations 6.6983528E-05 1.9357681E-02 at 40iterations 1.8505631E-05 5.5236816E-03 at 50iterations finished qdiffx linear iterations at : 11:35:11 total time elapsed so far: 5.100000 # loops : 50 mean,max change (kT/e) : 1.8505631E-05 5.5236816E-03 energy calculations done at 5.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.270000 DelPhi exited at 11:35:11 5.276u 0.469s 0:06.04 94.8% 0+0k 0+0io 4pf+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 11:35:12 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 = 2559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.613976 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): -10.51700 33.40000 ymin,ymax (A): -38.65000 27.52200 zmin,zma (A): -14.42900 38.99200 x,y,z range (A): 43.91700 66.17200 53.42100 scale (grids/A): 1.613976 object centre (A): 11.44150 -5.564000 12.28150 number of atom coordinates read : 2559 total number of charged atoms : 2410 net assigned charge : -1.499990 assigned positive charge : 373.1237 centred at (gu) : 92.16901 97.04465 94.54488 assigned negative charge : -374.6245 centred at (gu) : 92.19735 97.20026 94.60614 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 52238 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23272 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 14602 mr = 34262 m= 1172 mr = 9581 m= 20 mr = 504 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 94 time to turn everything in is 0.4700000 number of dielectric boundary points 23685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18392 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) : 0.5379919 object centre at (A) : 11.44150 -5.564000 12.28150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5184339E-03 5.2975112E-04 midg,1,midg; midg,igrid,midg 1.6339055E-03 2.8521284E-03 1,midg,midg; igrid,midg,midg -9.2045299E-04 1.7880071E-03 gauss-seidel spectral radius is 0.9980809 estimated iterations to convergence 181 setup time was (sec) 0.8600000 now iterating at: 11:35:13 rms-change max change #iterations 2.894775 141.7055 at 10iterations 1.167907 48.28836 at 20iterations 0.4750303 19.14639 at 30iterations 0.1931191 7.724641 at 40iterations 7.8498840E-02 3.129814 at 50iterations 3.1839438E-02 1.244483 at 60iterations 1.2993786E-02 0.5017147 at 70iterations 5.3096176E-03 0.2193470 at 80iterations 2.1859240E-03 8.9012146E-02 at 90iterations 9.1421907E-04 4.6764374E-02 at 100iterations 4.0369018E-04 1.9111633E-02 at 110iterations 1.9325266E-04 9.5915794E-03 at 120iterations finished qdiffx linear iterations at : 11:35:24 total time elapsed so far: 11.95000 # loops : 120 mean,max change (kT/e) : 1.9325266E-04 9.5915794E-03 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 11:35:24 12.124u 0.527s 0:12.95 97.6% 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 8 2011 at 11:35:25 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 = 2559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.420963 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): -10.51700 33.40000 ymin,ymax (A): -38.65000 27.52200 zmin,zma (A): -14.42900 38.99200 x,y,z range (A): 43.91700 66.17200 53.42100 scale (grids/A): 2.420963 object centre (A): 11.44150 -5.564000 12.28150 number of atom coordinates read : 2559 total number of charged atoms : 2410 net assigned charge : -1.499990 assigned positive charge : 373.1237 centred at (gu) : 93.25336 100.5669 96.81695 assigned negative charge : -374.6245 centred at (gu) : 93.29599 100.8004 96.90920 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 121644 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23272 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 52054 mr = 84618 m= 13062 mr = 40113 m= 1714 mr = 9343 m= 81 mr = 1043 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 336 time to turn everything in is 1.140000 number of dielectric boundary points 53419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 19247 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) : 1.613976 object centre at (A) : 11.44150 -5.564000 12.28150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6800928E-02 1.4522872E-02 midg,1,midg; midg,igrid,midg 6.9585919E-02 0.3888974 1,midg,midg; igrid,midg,midg -1.4960031E-02 2.1571046E-02 gauss-seidel spectral radius is 0.9990862 estimated iterations to convergence 261 setup time was (sec) 1.530000 now iterating at: 11:35:27 rms-change max change #iterations 7.568644 293.6476 at 10iterations 4.157808 129.9612 at 20iterations 2.260691 63.29269 at 30iterations 1.231949 32.70718 at 40iterations 0.6692906 18.06325 at 50iterations 0.3620164 8.964800 at 60iterations 0.1959665 4.452237 at 70iterations 0.1062321 2.498562 at 80iterations 5.7516240E-02 1.368682 at 90iterations 3.1014949E-02 0.6997223 at 100iterations 1.6772676E-02 0.4099998 at 110iterations 9.0788938E-03 0.2201538 at 120iterations 4.9327076E-03 0.1114635 at 130iterations 2.7021782E-03 6.3865662E-02 at 140iterations 1.4986405E-03 3.8816452E-02 at 150iterations 8.5320981E-04 2.4679184E-02 at 160iterations 5.0655444E-04 1.6749382E-02 at 170iterations 3.1882618E-04 1.0070086E-02 at 180iterations finished qdiffx linear iterations at : 11:35:44 total time elapsed so far: 19.47000 # loops : 180 mean,max change (kT/e) : 3.1882618E-04 1.0070086E-02 energy calculations done at 19.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.63000 DelPhi exited at 11:35:45 19.637u 0.528s 0:20.46 98.4% 0+0k 0+0io 0pf+0w