Sat Oct 8 18:11:30 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 Sat Oct 8 2011 at 18:11:30 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4704 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: 0.4966518 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): -0.9550000 62.11000 ymin,ymax (A): -30.01000 31.50400 zmin,zma (A): -22.24100 49.43900 x,y,z range (A): 63.06500 61.51400 71.68000 scale (grids/A): 0.4966518 object centre (A): 30.57750 0.7469997 13.59900 number of atom coordinates read : 4704 total number of charged atoms : 4549 net assigned charge : -11.99997 assigned positive charge : 723.5417 centred at (gu) : 90.57902 91.07027 89.88657 assigned negative charge : -735.5471 centred at (gu) : 90.58634 91.03105 89.88357 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7510 nv = 96 ne = 84 npr = 91821 no. pairs analyzed = 91821 no. exposed pairs = 6308 no. arc points = 43869 no. surface atoms = 2094 nbur = 2610 mkacc time = 0.1600000 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 = 1.708000 m= 264 mr = 3677 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4253 ## 674 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10054 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7589374E-11 -8.3522522E-11 midg,1,midg; midg,igrid,midg -1.1090810E-10 -4.4142190E-11 1,midg,midg; igrid,midg,midg -6.8621595E-11 -1.1772569E-10 gauss-seidel spectral radius is 0.9792805 estimated iterations to convergence 58 setup time was (sec) 0.5300000 now iterating at: 18:11:31 rms-change max change #iterations 5.8479507E-02 10.32784 at 10iterations 3.2067578E-03 0.5166836 at 20iterations 3.2782997E-04 6.4353943E-02 at 30iterations 7.6105782E-05 1.4314651E-02 at 40iterations 1.9780169E-05 3.6344528E-03 at 50iterations finished qdiffx linear iterations at : 18:11:34 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 1.9780169E-05 3.6344528E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 18:11:34 3.728u 0.174s 0:04.18 93.0% 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 Sat Oct 8 2011 at 18:11:34 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4704 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: 1.489955 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): -0.9550000 62.11000 ymin,ymax (A): -30.01000 31.50400 zmin,zma (A): -22.24100 49.43900 x,y,z range (A): 63.06500 61.51400 71.68000 scale (grids/A): 1.489955 object centre (A): 30.57750 0.7469997 13.59900 number of atom coordinates read : 4704 total number of charged atoms : 4549 net assigned charge : -11.99997 assigned positive charge : 723.5417 centred at (gu) : 91.73537 93.20932 89.65796 assigned negative charge : -735.5471 centred at (gu) : 91.75884 93.09306 89.65057 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 84635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43869 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 23591 mr = 56114 m= 1798 mr = 15025 m= 28 mr = 677 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.4100000 number of dielectric boundary points 38236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 642 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 33867 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) : 0.4966518 object centre at (A) : 30.57750 0.7469997 13.59900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3904195E-04 -1.6605929E-02 midg,1,midg; midg,igrid,midg -1.2261461E-02 -7.5779869E-03 1,midg,midg; igrid,midg,midg 3.7823294E-03 -2.0605738E-03 gauss-seidel spectral radius is 0.9979928 estimated iterations to convergence 177 setup time was (sec) 0.6500000 now iterating at: 18:11:35 rms-change max change #iterations 3.583773 182.9135 at 10iterations 1.426141 52.05334 at 20iterations 0.5651600 21.93064 at 30iterations 0.2255876 7.454216 at 40iterations 9.0020068E-02 2.891993 at 50iterations 3.6042843E-02 1.202534 at 60iterations 1.4435210E-02 0.4904633 at 70iterations 5.7508610E-03 0.1928827 at 80iterations 2.3298291E-03 7.3204041E-02 at 90iterations 9.5099519E-04 3.2386780E-02 at 100iterations 3.9803085E-04 1.3105869E-02 at 110iterations 1.7435332E-04 6.6032410E-03 at 120iterations finished qdiffx linear iterations at : 18:11:43 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 1.7435332E-04 6.6032410E-03 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 18:11:43 8.383u 0.236s 0:08.91 96.6% 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 18:11:43 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4704 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: 2.234933 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): -0.9550000 62.11000 ymin,ymax (A): -30.01000 31.50400 zmin,zma (A): -22.24100 49.43900 x,y,z range (A): 63.06500 61.51400 71.68000 scale (grids/A): 2.234933 object centre (A): 30.57750 0.7469997 13.59900 number of atom coordinates read : 4704 total number of charged atoms : 4549 net assigned charge : -11.99997 assigned positive charge : 723.5417 centred at (gu) : 92.60282 94.81346 89.48665 assigned negative charge : -735.5471 centred at (gu) : 92.63793 94.63943 89.47583 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 197253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43869 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 85682 mr = 138837 m= 20217 mr = 65123 m= 2395 mr = 13986 m= 88 mr = 1298 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 483 time to turn everything in is 1.010000 number of dielectric boundary points 86387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 36250 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) : 1.489955 object centre at (A) : 30.57750 0.7469997 13.59900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1498945 -0.2205660 midg,1,midg; midg,igrid,midg -0.2942704 -0.1338631 1,midg,midg; igrid,midg,midg 8.2707435E-02 -7.4678183E-02 gauss-seidel spectral radius is 0.9991246 estimated iterations to convergence 267 setup time was (sec) 1.270000 now iterating at: 18:11:45 rms-change max change #iterations 10.06132 298.1201 at 10iterations 5.745169 153.8180 at 20iterations 3.244672 78.98743 at 30iterations 1.819951 44.61641 at 40iterations 1.013816 20.28672 at 50iterations 0.5644799 12.16777 at 60iterations 0.3121668 6.447246 at 70iterations 0.1720987 3.390842 at 80iterations 9.5090657E-02 2.059379 at 90iterations 5.2434318E-02 1.017982 at 100iterations 2.8839780E-02 0.5978584 at 110iterations 1.5828170E-02 0.3105283 at 120iterations 8.7168198E-03 0.1848373 at 130iterations 4.7821808E-03 9.6608162E-02 at 140iterations 2.6222935E-03 4.9976349E-02 at 150iterations 1.4403050E-03 2.7587891E-02 at 160iterations 7.8866282E-04 1.4853477E-02 at 170iterations 4.3284785E-04 8.0189705E-03 at 180iterations finished qdiffx linear iterations at : 18:11:57 total time elapsed so far: 13.74000 # loops : 180 mean,max change (kT/e) : 4.3284785E-04 8.0189705E-03 energy calculations done at 13.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.87000 DelPhi exited at 18:11:58 13.868u 0.253s 0:14.39 98.0% 0+0k 0+0io 0pf+0w