Wed Dec 21 14:21:26 PST 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 Wed Dec 21 2011 at 14:21:28 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6478735 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): -4.966000 34.23200 ymin,ymax (A): -3.439000 49.61500 zmin,zma (A): -23.77200 31.17700 x,y,z range (A): 39.19800 53.05400 54.94900 scale (grids/A): 0.6478735 object centre (A): 14.63300 23.08800 3.702500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 90.44278 92.05909 89.99898 assigned negative charge : -284.4403 centred at (gu) : 90.55940 92.20848 89.91640 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5664 nv = 96 ne = 84 npr = 40436 no. pairs analyzed = 40436 no. exposed pairs = 2456 no. arc points = 17189 no. surface atoms = 833 nbur = 1133 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 270 mr = 3147 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2600000 number of dielectric boundary points 2748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1740 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2141098E-09 1.5137879E-08 midg,1,midg; midg,igrid,midg 1.4274732E-08 -1.5015672E-08 1,midg,midg; igrid,midg,midg 1.6977884E-08 -6.4962054E-09 gauss-seidel spectral radius is 0.9875985 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 14:21:29 rms-change max change #iterations 0.1283918 24.74473 at 10iterations 1.2819614E-02 1.949783 at 20iterations 1.2995822E-03 0.2240086 at 30iterations 1.3577686E-04 2.1880627E-02 at 40iterations 1.3350655E-05 2.4700165E-03 at 50iterations finished qdiffx linear iterations at : 14:21:32 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 1.3350655E-05 2.4700165E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 14:21:35 4.436u 0.426s 0:07.77 62.4% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:36 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.943621 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): -4.966000 34.23200 ymin,ymax (A): -3.439000 49.61500 zmin,zma (A): -23.77200 31.17700 x,y,z range (A): 39.19800 53.05400 54.94900 scale (grids/A): 1.943621 object centre (A): 14.63300 23.08800 3.702500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 91.32860 96.17731 89.99712 assigned negative charge : -284.4403 centred at (gu) : 91.67850 96.62569 89.74928 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 60587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17189 grid for indexing accessible points = 1.400000 m= 22087 mr = 41773 m= 3205 mr = 16898 m= 143 mr = 2012 m= 3 mr = 43 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2296 time to turn everything in is 0.6000000 number of dielectric boundary points 25300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14462 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) : 0.6478735 object centre at (A) : 14.63300 23.08800 3.702500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4901468E-02 1.6453626E-02 midg,1,midg; midg,igrid,midg 4.6974894E-02 -1.2989385E-02 1,midg,midg; igrid,midg,midg 8.6467946E-03 -4.5525301E-03 gauss-seidel spectral radius is 0.9986104 estimated iterations to convergence 213 setup time was (sec) 1.000000 now iterating at: 14:21:38 rms-change max change #iterations 3.679488 167.3276 at 10iterations 1.708948 85.83702 at 20iterations 0.7968918 29.48876 at 30iterations 0.3702468 12.90958 at 40iterations 0.1722879 5.894905 at 50iterations 7.9890102E-02 2.832959 at 60iterations 3.7205134E-02 1.261874 at 70iterations 1.7284866E-02 0.6136169 at 80iterations 8.0258306E-03 0.2649584 at 90iterations 3.7338107E-03 0.1301441 at 100iterations 1.7447597E-03 6.0746193E-02 at 110iterations 8.0855604E-04 2.7137756E-02 at 120iterations finished qdiffx linear iterations at : 14:21:51 total time elapsed so far: 14.30000 # loops : 120 mean,max change (kT/e) : 8.0855604E-04 2.7137756E-02 energy calculations done at 14.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.50000 DelPhi exited at 14:21:58 14.501u 0.851s 0:22.50 68.2% 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 Wed Dec 21 2011 at 14:22:01 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.915431 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): -4.966000 34.23200 ymin,ymax (A): -3.439000 49.61500 zmin,zma (A): -23.77200 31.17700 x,y,z range (A): 39.19800 53.05400 54.94900 scale (grids/A): 2.915431 object centre (A): 14.63300 23.08800 3.702500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 91.99296 99.26592 89.99585 assigned negative charge : -284.4403 centred at (gu) : 92.51793 99.93851 89.62404 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 139889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17189 grid for indexing accessible points = 1.400000 m= 71495 mr = 100975 m= 25753 mr = 59413 m= 5598 mr = 21383 m= 661 mr = 4231 m= 40 mr = 424 m= 0 mr = 15 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 7670 time to turn everything in is 1.280000 number of dielectric boundary points 56995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 14656 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) : 1.943621 object centre at (A) : 14.63300 23.08800 3.702500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.000872 2.1305826E-02 midg,1,midg; midg,igrid,midg 0.4914011 -0.1777108 1,midg,midg; igrid,midg,midg 5.7749830E-02 -2.5574811E-02 gauss-seidel spectral radius is 0.9992374 estimated iterations to convergence 286 setup time was (sec) 1.600000 now iterating at: 14:22:04 rms-change max change #iterations 8.624699 429.0267 at 10iterations 4.949458 138.8369 at 20iterations 2.820590 63.18037 at 30iterations 1.610348 36.43568 at 40iterations 0.9184101 24.75694 at 50iterations 0.5226922 10.71533 at 60iterations 0.2969558 6.201757 at 70iterations 0.1685493 3.490686 at 80iterations 9.6400857E-02 2.203733 at 90iterations 5.4704659E-02 1.061074 at 100iterations 3.1112228E-02 0.6397552 at 110iterations 1.7608132E-02 0.3462963 at 120iterations 1.0033548E-02 0.1891098 at 130iterations 5.6915600E-03 0.1039534 at 140iterations 3.2460454E-03 7.5746536E-02 at 150iterations 1.8453778E-03 3.8898468E-02 at 160iterations 1.0480793E-03 2.2838593E-02 at 170iterations 5.9756404E-04 1.1593819E-02 at 180iterations finished qdiffx linear iterations at : 14:22:31 total time elapsed so far: 28.88000 # loops : 180 mean,max change (kT/e) : 5.9756404E-04 1.1593819E-02 energy calculations done at 28.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.07000 DelPhi exited at 14:22:35 29.075u 0.566s 0:34.47 85.9% 0+0k 0+0io 0pf+0w