Sun Oct 9 02:57:29 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 Sun Oct 9 2011 at 02:57:29 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4462 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4364564 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): -3.425000 78.14100 ymin,ymax (A): 1.107000 65.35400 zmin,zma (A): 166.5010 227.0740 x,y,z range (A): 81.56600 64.24699 60.57298 scale (grids/A): 0.4364564 object centre (A): 37.35800 33.23050 196.7875 number of atom coordinates read : 4462 total number of charged atoms : 4231 net assigned charge : 21.00000 assigned positive charge : 653.9194 centred at (gu) : 85.91937 91.13241 88.87552 assigned negative charge : -632.9240 centred at (gu) : 85.90594 91.09718 88.89743 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 5094 nv = 96 ne = 84 npr = 90506 no. pairs analyzed = 90506 no. exposed pairs = 5666 no. arc points = 39639 no. surface atoms = 1942 nbur = 2520 mkacc time = 0.2600000 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 = 1.932000 m= 132 mr = 2405 m= 0 mr = 1 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 2820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3257 ## 671 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 6876 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0227682E-11 3.5227875E-12 midg,1,midg; midg,igrid,midg 2.9958603E-12 1.1278018E-11 1,midg,midg; igrid,midg,midg 1.8448097E-11 2.0775716E-12 gauss-seidel spectral radius is 0.9732140 estimated iterations to convergence 51 setup time was (sec) 0.8100000 now iterating at: 02:57:31 rms-change max change #iterations 2.8455142E-02 5.411814 at 10iterations 2.5105968E-03 0.4687138 at 20iterations 6.7890889E-04 0.1368532 at 30iterations 1.9762943E-04 4.0351868E-02 at 40iterations 5.7706588E-05 1.1840820E-02 at 50iterations finished qdiffx linear iterations at : 02:57:34 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 5.7706588E-05 1.1840820E-02 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 02:57:35 4.523u 0.282s 0:05.10 94.1% 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 02:57:35 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4462 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.309369 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): -3.425000 78.14100 ymin,ymax (A): 1.107000 65.35400 zmin,zma (A): 166.5010 227.0740 x,y,z range (A): 81.56600 64.24699 60.57298 scale (grids/A): 1.309369 object centre (A): 37.35800 33.23050 196.7875 number of atom coordinates read : 4462 total number of charged atoms : 4231 net assigned charge : 21.00000 assigned positive charge : 653.9194 centred at (gu) : 77.75648 93.39572 86.62504 assigned negative charge : -632.9240 centred at (gu) : 77.71746 93.29111 86.69220 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 59188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39639 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 13714 mr = 38918 m= 690 mr = 8097 m= 6 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 454 time to turn everything in is 0.5900000 number of dielectric boundary points 26428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 730 ## 31 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 29707 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) : 0.4364564 object centre at (A) : 37.35800 33.23050 196.7875 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3084021E-03 6.7424861E-04 midg,1,midg; midg,igrid,midg 1.6644860E-03 2.7848966E-03 1,midg,midg; igrid,midg,midg 2.3925193E-02 3.3082881E-03 gauss-seidel spectral radius is 0.9972546 estimated iterations to convergence 152 setup time was (sec) 0.8900000 now iterating at: 02:57:36 rms-change max change #iterations 2.405463 114.7770 at 10iterations 0.8231524 41.27088 at 20iterations 0.2820617 11.84433 at 30iterations 9.6532226E-02 4.214975 at 40iterations 3.3375762E-02 1.413307 at 50iterations 1.1651614E-02 0.4569163 at 60iterations 4.3128850E-03 0.2028694 at 70iterations 1.8316408E-03 8.2038879E-02 at 80iterations 9.5127214E-04 4.2316437E-02 at 90iterations 5.8172218E-04 2.4950027E-02 at 100iterations 3.8096530E-04 1.6275406E-02 at 110iterations 2.5394236E-04 1.0784149E-02 at 120iterations finished qdiffx linear iterations at : 02:57:44 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 2.5394236E-04 1.0784149E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 02:57:45 9.568u 0.358s 0:10.19 97.2% 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 Sun Oct 9 2011 at 02:57:45 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4462 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.964054 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): -3.425000 78.14100 ymin,ymax (A): 1.107000 65.35400 zmin,zma (A): 166.5010 227.0740 x,y,z range (A): 81.56600 64.24699 60.57298 scale (grids/A): 1.964054 object centre (A): 37.35800 33.23050 196.7875 number of atom coordinates read : 4462 total number of charged atoms : 4231 net assigned charge : 21.00000 assigned positive charge : 653.9194 centred at (gu) : 71.63432 95.09304 84.93719 assigned negative charge : -632.9240 centred at (gu) : 71.57617 94.93657 85.03812 start vw surface at 0.2100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 139028 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39639 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 53260 mr = 97300 m= 9766 mr = 39267 m= 717 mr = 6160 m= 15 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 1526 time to turn everything in is 1.360000 number of dielectric boundary points 59773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 33451 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) : 1.309369 object centre at (A) : 37.35800 33.23050 196.7875 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7662075E-02 1.4329515E-02 midg,1,midg; midg,igrid,midg 3.7924211E-02 3.2158412E-02 1,midg,midg; igrid,midg,midg 0.5760118 3.6997706E-02 gauss-seidel spectral radius is 0.9988520 estimated iterations to convergence 234 setup time was (sec) 1.680000 now iterating at: 02:57:47 rms-change max change #iterations 7.232273 229.0840 at 10iterations 3.733315 116.8214 at 20iterations 1.915164 55.98561 at 30iterations 0.9790322 31.42690 at 40iterations 0.4966723 12.39553 at 50iterations 0.2521838 7.394732 at 60iterations 0.1276269 3.260251 at 70iterations 6.4264819E-02 1.571506 at 80iterations 3.2419894E-02 0.8690948 at 90iterations 1.6355872E-02 0.4021416 at 100iterations 8.2301609E-03 0.2135744 at 110iterations 4.1651772E-03 0.1060696 at 120iterations 2.1330279E-03 5.3818464E-02 at 130iterations 1.1117951E-03 3.2815456E-02 at 140iterations 6.0060067E-04 1.4582634E-02 at 150iterations 3.4819025E-04 9.3688965E-03 at 160iterations 2.1999548E-04 6.4563751E-03 at 170iterations 1.5002309E-04 3.7784576E-03 at 180iterations finished qdiffx linear iterations at : 02:58:00 total time elapsed so far: 15.25000 # loops : 180 mean,max change (kT/e) : 1.5002309E-04 3.7784576E-03 energy calculations done at 15.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 02:58:01 15.422u 0.342s 0:16.02 98.3% 0+0k 0+0io 0pf+0w