Sun Oct 9 08:15:13 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 08:15:13 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4167 !!! WARNING: NDP 2113 has a net charge of -3.0000 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: 0.3286862 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): -28.02000 80.29000 ymin,ymax (A): -40.84200 24.62400 zmin,zma (A): -16.78400 83.00500 x,y,z range (A): 108.3100 65.46600 99.78900 scale (grids/A): 0.3286862 object centre (A): 26.13500 -8.108999 33.11050 number of atom coordinates read : 4167 total number of charged atoms : 3687 net assigned charge : 7.500025 assigned positive charge : 573.8572 centred at (gu) : 81.64444 91.74670 85.13872 assigned negative charge : -566.3599 centred at (gu) : 81.61578 91.66621 85.26637 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 2582 nv = 96 ne = 84 npr = 79735 no. pairs analyzed = 79735 no. exposed pairs = 5874 no. arc points = 43771 no. surface atoms = 1967 nbur = 2200 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 = 2.520000 m= 44 mr = 927 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 1699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2144 ## 715 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 3369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0620902E-14 -1.4387932E-16 midg,1,midg; midg,igrid,midg -2.5115504E-16 2.0543535E-15 1,midg,midg; igrid,midg,midg -1.3040808E-15 2.3252806E-17 gauss-seidel spectral radius is 0.9534234 estimated iterations to convergence 39 setup time was (sec) 0.4500000 now iterating at: 08:15:14 rms-change max change #iterations 5.0224955E-03 1.986367 at 10iterations 1.6310799E-04 5.6783676E-02 at 20iterations 1.4782927E-05 4.8418045E-03 at 30iterations 1.5375192E-06 4.8160553E-04 at 40iterations 1.7109882E-07 6.6757202E-05 at 50iterations finished qdiffx linear iterations at : 08:15:18 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 1.7109882E-07 6.6757202E-05 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 08:15:18 4.378u 0.196s 0:04.91 92.8% 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 08:15:18 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4167 !!! WARNING: NDP 2113 has a net charge of -3.0000 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: 0.9860585 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): -28.02000 80.29000 ymin,ymax (A): -40.84200 24.62400 zmin,zma (A): -16.78400 83.00500 x,y,z range (A): 108.3100 65.46600 99.78900 scale (grids/A): 0.9860585 object centre (A): 26.13500 -8.108999 33.11050 number of atom coordinates read : 4167 total number of charged atoms : 3687 net assigned charge : 7.500025 assigned positive charge : 573.8572 centred at (gu) : 64.93200 95.23902 75.41486 assigned negative charge : -566.3599 centred at (gu) : 64.84695 94.99818 75.79893 start vw surface at 0.1100000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 31406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43771 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.352000 m= 4134 mr = 17609 m= 72 mr = 1604 m= 0 mr = 2 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 399 time to turn everything in is 0.2200000 number of dielectric boundary points 16397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1173 ## 96 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 21484 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) : 0.3286862 object centre at (A) : 26.13500 -8.108999 33.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5138389E-04 -4.5904896E-04 midg,1,midg; midg,igrid,midg -1.1878474E-05 4.5877812E-05 1,midg,midg; igrid,midg,midg 3.4872798E-04 4.6941423E-06 gauss-seidel spectral radius is 0.9947938 estimated iterations to convergence 111 setup time was (sec) 0.4300000 now iterating at: 08:15:19 rms-change max change #iterations 0.9614729 117.5312 at 10iterations 0.2181077 19.52516 at 20iterations 4.9881823E-02 4.050833 at 30iterations 1.1317114E-02 0.7556415 at 40iterations 2.5859713E-03 0.1605339 at 50iterations 6.1029132E-04 3.8713038E-02 at 60iterations 1.5361000E-04 9.6378326E-03 at 70iterations 4.3483673E-05 2.7923584E-03 at 80iterations 1.5150107E-05 9.1433525E-04 at 90iterations 6.0234993E-06 3.5095215E-04 at 100iterations 2.5326890E-06 1.5640259E-04 at 110iterations 1.1242083E-06 7.0571899E-05 at 120iterations finished qdiffx linear iterations at : 08:15:26 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 1.1242083E-06 7.0571899E-05 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 08:15:26 7.400u 0.199s 0:08.07 94.0% 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 08:15:26 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4167 !!! WARNING: NDP 2113 has a net charge of -3.0000 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: 1.479088 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): -28.02000 80.29000 ymin,ymax (A): -40.84200 24.62400 zmin,zma (A): -16.78400 83.00500 x,y,z range (A): 108.3100 65.46600 99.78900 scale (grids/A): 1.479088 object centre (A): 26.13500 -8.108999 33.11050 number of atom coordinates read : 4167 total number of charged atoms : 3687 net assigned charge : 7.500025 assigned positive charge : 573.8572 centred at (gu) : 52.39788 97.85830 68.12199 assigned negative charge : -566.3599 centred at (gu) : 52.27037 97.49718 68.69826 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 74453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43771 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.324000 m= 18767 mr = 45456 m= 1290 mr = 11499 m= 29 mr = 414 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1380 time to turn everything in is 0.4200000 number of dielectric boundary points 37170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 494 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 27437 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) : 0.9860585 object centre at (A) : 26.13500 -8.108999 33.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7780862E-02 -9.3990965E-03 midg,1,midg; midg,igrid,midg 9.8490209E-06 1.6966369E-03 1,midg,midg; igrid,midg,midg -0.1005155 2.1377405E-04 gauss-seidel spectral radius is 0.9976728 estimated iterations to convergence 165 setup time was (sec) 0.6400000 now iterating at: 08:15:27 rms-change max change #iterations 3.562839 214.8572 at 10iterations 1.392249 83.66669 at 20iterations 0.5382656 31.67126 at 30iterations 0.2054587 9.023533 at 40iterations 7.8070208E-02 3.073841 at 50iterations 2.9507022E-02 1.323833 at 60iterations 1.1152824E-02 0.4827521 at 70iterations 4.1852980E-03 0.1910563 at 80iterations 1.5704695E-03 6.3766479E-02 at 90iterations 5.8841647E-04 2.8185844E-02 at 100iterations 2.2066018E-04 8.2225800E-03 at 110iterations 8.2919963E-05 3.1747818E-03 at 120iterations 3.1015697E-05 1.1100769E-03 at 130iterations 1.1632755E-05 4.9209595E-04 at 140iterations 4.4245321E-06 1.7929077E-04 at 150iterations 1.8125621E-06 6.8664551E-05 at 160iterations 1.0025310E-06 6.1035156E-05 at 170iterations 8.2627724E-07 6.1035156E-05 at 180iterations finished qdiffx linear iterations at : 08:15:38 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 8.2627724E-07 6.1035156E-05 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 08:15:38 11.268u 0.205s 0:11.78 97.2% 0+0k 0+0io 0pf+0w