Tue Oct 11 02:22:00 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 Tue Oct 11 2011 at 02:22:00 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: FMN 402 has a net charge of -2.0000 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: 0.6824760 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): -56.22300 -4.060000 ymin,ymax (A): -42.22700 3.574000 zmin,zma (A): -30.80800 17.49600 x,y,z range (A): 52.16300 45.80100 48.30400 scale (grids/A): 0.6824760 object centre (A): -30.14150 -19.32650 -6.656000 number of atom coordinates read : 2656 total number of charged atoms : 2521 net assigned charge : 3.500016 assigned positive charge : 408.1055 centred at (gu) : 88.73378 90.22969 89.83635 assigned negative charge : -404.6065 centred at (gu) : 89.02673 90.21015 89.79900 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8328 nv = 96 ne = 84 npr = 55037 no. pairs analyzed = 55037 no. exposed pairs = 3244 no. arc points = 22355 no. surface atoms = 1087 nbur = 1569 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 540 mr = 4776 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.3500000 number of dielectric boundary points 4008 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2142 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9704 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2010969E-09 2.7173497E-08 midg,1,midg; midg,igrid,midg 7.3292723E-09 2.2709397E-08 1,midg,midg; igrid,midg,midg 1.5182246E-07 -7.2305269E-08 gauss-seidel spectral radius is 0.9888726 estimated iterations to convergence 77 setup time was (sec) 0.6200000 now iterating at: 02:22:01 rms-change max change #iterations 0.1988600 27.59399 at 10iterations 2.3695620E-02 3.096764 at 20iterations 3.8797818E-03 0.6428070 at 30iterations 1.2553245E-03 0.2550011 at 40iterations 5.1595527E-04 0.1068153 at 50iterations finished qdiffx linear iterations at : 02:22:04 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 5.1595527E-04 0.1068153 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 02:22:05 4.064u 0.265s 0:05.20 83.0% 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 Tue Oct 11 2011 at 02:22:05 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: FMN 402 has a net charge of -2.0000 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: 2.047428 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): -56.22300 -4.060000 ymin,ymax (A): -42.22700 3.574000 zmin,zma (A): -30.80800 17.49600 x,y,z range (A): 52.16300 45.80100 48.30400 scale (grids/A): 2.047428 object centre (A): -30.14150 -19.32650 -6.656000 number of atom coordinates read : 2656 total number of charged atoms : 2521 net assigned charge : 3.500016 assigned positive charge : 408.1055 centred at (gu) : 86.20049 90.68851 89.50813 assigned negative charge : -404.6065 centred at (gu) : 87.08010 90.63033 89.39679 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 88870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22355 grid for indexing accessible points = 1.400000 m= 34510 mr = 62801 m= 6364 mr = 26053 m= 570 mr = 4215 m= 11 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 296 time to turn everything in is 0.7900000 number of dielectric boundary points 36948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 19989 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) : 0.6824760 object centre at (A) : -30.14150 -19.32650 -6.656000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1605722E-02 -2.3455715E-02 midg,1,midg; midg,igrid,midg 2.0076083E-02 3.5170343E-02 1,midg,midg; igrid,midg,midg 9.1014937E-02 -5.7122860E-02 gauss-seidel spectral radius is 0.9988169 estimated iterations to convergence 230 setup time was (sec) 1.080000 now iterating at: 02:22:06 rms-change max change #iterations 5.025486 198.7975 at 10iterations 2.470129 81.60183 at 20iterations 1.217192 35.38148 at 30iterations 0.6005856 19.13320 at 40iterations 0.2966649 9.082779 at 50iterations 0.1465990 3.981793 at 60iterations 7.2591126E-02 2.044168 at 70iterations 3.6136195E-02 1.041006 at 80iterations 1.8130597E-02 0.5429277 at 90iterations 9.2954626E-03 0.2667160 at 100iterations 4.9114870E-03 0.1760750 at 110iterations 2.7727729E-03 9.9617004E-02 at 120iterations finished qdiffx linear iterations at : 02:22:15 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 2.7727729E-03 9.9617004E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 02:22:16 9.603u 0.306s 0:10.74 92.1% 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 Tue Oct 11 2011 at 02:22:16 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: FMN 402 has a net charge of -2.0000 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: 3.071142 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): -56.22300 -4.060000 ymin,ymax (A): -42.22700 3.574000 zmin,zma (A): -30.80800 17.49600 x,y,z range (A): 52.16300 45.80100 48.30400 scale (grids/A): 3.071142 object centre (A): -30.14150 -19.32650 -6.656000 number of atom coordinates read : 2656 total number of charged atoms : 2521 net assigned charge : 3.500016 assigned positive charge : 408.1055 centred at (gu) : 84.30062 91.03247 89.26205 assigned negative charge : -404.6065 centred at (gu) : 85.62006 90.94543 89.09502 start vw surface at 0.1500000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 205234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22355 grid for indexing accessible points = 1.400000 m= 108161 mr = 151466 m= 43394 mr = 89743 m= 11776 mr = 35674 m= 2174 mr = 9040 m= 240 mr = 1551 m= 9 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 1081 time to turn everything in is 2.100000 number of dielectric boundary points 83352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 20168 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) : 2.047428 object centre at (A) : -30.14150 -19.32650 -6.656000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4496831 -0.2946804 midg,1,midg; midg,igrid,midg 0.1272547 0.4158133 1,midg,midg; igrid,midg,midg 0.5864633 -0.6849294 gauss-seidel spectral radius is 0.9993032 estimated iterations to convergence 299 setup time was (sec) 2.420000 now iterating at: 02:22:18 rms-change max change #iterations 11.33297 416.8909 at 10iterations 6.700375 138.5079 at 20iterations 3.957024 79.26518 at 30iterations 2.334700 46.37906 at 40iterations 1.374067 23.47046 at 50iterations 0.8089947 16.41813 at 60iterations 0.4744570 8.748089 at 70iterations 0.2786867 4.354067 at 80iterations 0.1632733 3.047298 at 90iterations 9.5996588E-02 1.769413 at 100iterations 5.6401059E-02 0.9769430 at 110iterations 3.3205796E-02 0.6549606 at 120iterations 1.9756045E-02 0.3509827 at 130iterations 1.1897619E-02 0.2482948 at 140iterations 7.3650670E-03 0.1585312 at 150iterations 4.7741123E-03 0.1101906 at 160iterations 3.2993138E-03 8.3740234E-02 at 170iterations 2.4359403E-03 6.3964844E-02 at 180iterations finished qdiffx linear iterations at : 02:22:32 total time elapsed so far: 16.31000 # loops : 180 mean,max change (kT/e) : 2.4359403E-03 6.3964844E-02 energy calculations done at 16.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.49000 DelPhi exited at 02:22:33 16.489u 0.318s 0:17.39 96.5% 0+0k 0+0io 0pf+0w