Mon Oct 10 09:51:13 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+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 Mon Oct 10 2011 at 09:51:14 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2804 !!! WARNING: HIT 226 has a net charge of 0.5140 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: 0.5836927 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): -17.04000 36.39000 ymin,ymax (A): -64.74600 -4.804000 zmin,zma (A): -3.715000 57.27600 x,y,z range (A): 53.43000 59.94200 60.99100 scale (grids/A): 0.5836927 object centre (A): 9.674999 -34.77500 26.78050 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 8.014018 assigned positive charge : 411.4630 centred at (gu) : 88.75874 89.75729 87.32899 assigned negative charge : -403.4493 centred at (gu) : 88.85291 89.68662 87.23272 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6406 nv = 96 ne = 84 npr = 54769 no. pairs analyzed = 54769 no. exposed pairs = 4293 no. arc points = 31724 no. surface atoms = 1408 nbur = 1396 mkacc time = 0.1200000 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= 324 mr = 2719 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3144 ## 352 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2886347E-10 2.2514457E-09 midg,1,midg; midg,igrid,midg 4.4018988E-10 3.3811143E-09 1,midg,midg; igrid,midg,midg 5.4615850E-09 -6.3274441E-11 gauss-seidel spectral radius is 0.9848528 estimated iterations to convergence 67 setup time was (sec) 0.5000000 now iterating at: 09:51:14 rms-change max change #iterations 9.4574779E-02 14.28113 at 10iterations 7.4006151E-03 1.359008 at 20iterations 6.0898950E-04 0.1027428 at 30iterations 6.0878345E-05 9.6359253E-03 at 40iterations 9.6502727E-06 1.1043549E-03 at 50iterations finished qdiffx linear iterations at : 09:51:17 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 9.6502727E-06 1.1043549E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 09:51:17 3.077u 0.146s 0:03.50 91.7% 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 09:51:17 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2804 !!! WARNING: HIT 226 has a net charge of 0.5140 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: 1.751078 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): -17.04000 36.39000 ymin,ymax (A): -64.74600 -4.804000 zmin,zma (A): -3.715000 57.27600 x,y,z range (A): 53.43000 59.94200 60.99100 scale (grids/A): 1.751078 object centre (A): 9.674999 -34.77500 26.78050 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 8.014018 assigned positive charge : 411.4630 centred at (gu) : 86.27592 89.27162 81.98653 assigned negative charge : -403.4493 centred at (gu) : 86.55853 89.05926 81.69781 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31724 grid for indexing accessible points = 1.400000 m= 21933 mr = 41002 m= 3038 mr = 13844 m= 125 mr = 1463 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 37020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 20657 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) : 0.5836927 object centre at (A) : 9.674999 -34.77500 26.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0031483E-04 4.3408712E-03 midg,1,midg; midg,igrid,midg 2.4728864E-02 4.2319182E-02 1,midg,midg; igrid,midg,midg 1.8738739E-02 5.2798921E-03 gauss-seidel spectral radius is 0.9984322 estimated iterations to convergence 200 setup time was (sec) 0.7500000 now iterating at: 09:51:18 rms-change max change #iterations 3.715140 165.1887 at 10iterations 1.640994 62.11581 at 20iterations 0.7238417 24.89558 at 30iterations 0.3201095 10.86788 at 40iterations 0.1417842 5.356895 at 50iterations 6.2390339E-02 2.027107 at 60iterations 2.7651019E-02 0.9666138 at 70iterations 1.2195251E-02 0.4621620 at 80iterations 5.3955987E-03 0.1799164 at 90iterations 2.4018150E-03 8.3194733E-02 at 100iterations 1.0623700E-03 3.7246704E-02 at 110iterations 4.7103403E-04 1.6177177E-02 at 120iterations finished qdiffx linear iterations at : 09:51:24 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 4.7103403E-04 1.6177177E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 09:51:25 6.869u 0.190s 0:07.62 92.5% 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 09:51:25 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2804 !!! WARNING: HIT 226 has a net charge of 0.5140 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: 2.626617 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): -17.04000 36.39000 ymin,ymax (A): -64.74600 -4.804000 zmin,zma (A): -3.715000 57.27600 x,y,z range (A): 53.43000 59.94200 60.99100 scale (grids/A): 2.626617 object centre (A): 9.674999 -34.77500 26.78050 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 8.014018 assigned positive charge : 411.4630 centred at (gu) : 84.41373 88.90713 77.97970 assigned negative charge : -403.4493 centred at (gu) : 84.83758 88.58889 77.54675 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 157592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31724 grid for indexing accessible points = 1.400000 m= 71109 mr = 101448 m= 23737 mr = 52397 m= 5041 mr = 17237 m= 547 mr = 3149 m= 16 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 83582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 21220 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) : 1.751078 object centre at (A) : 9.674999 -34.77500 26.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2246694E-02 4.1740585E-02 midg,1,midg; midg,igrid,midg 0.6108514 0.5001692 1,midg,midg; igrid,midg,midg 0.1569664 7.9861194E-02 gauss-seidel spectral radius is 0.9992312 estimated iterations to convergence 285 setup time was (sec) 1.460000 now iterating at: 09:51:26 rms-change max change #iterations 9.407992 336.7458 at 10iterations 5.571030 160.0528 at 20iterations 3.246669 90.36519 at 30iterations 1.882641 47.24682 at 40iterations 1.086555 27.15888 at 50iterations 0.6256377 18.29887 at 60iterations 0.3581128 8.129473 at 70iterations 0.2047893 5.390127 at 80iterations 0.1170295 3.003487 at 90iterations 6.6758849E-02 1.395975 at 100iterations 3.8020317E-02 0.7861691 at 110iterations 2.1693625E-02 0.4832735 at 120iterations 1.2301340E-02 0.2676220 at 130iterations 7.0000966E-03 0.1387720 at 140iterations 3.9771353E-03 7.9963684E-02 at 150iterations 2.2589026E-03 4.3970108E-02 at 160iterations 1.2842321E-03 3.1305313E-02 at 170iterations 7.3068816E-04 1.5406132E-02 at 180iterations finished qdiffx linear iterations at : 09:51:36 total time elapsed so far: 10.96000 # loops : 180 mean,max change (kT/e) : 7.3068816E-04 1.5406132E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 09:51:36 11.132u 0.171s 0:11.64 97.0% 0+0k 0+0io 0pf+0w