Sun Oct 9 14:46:24 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 Sun Oct 9 2011 at 14:46:24 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 0.6095995 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): -21.36600 37.03300 ymin,ymax (A): -24.00900 26.67100 zmin,zma (A): -10.02800 38.69900 x,y,z range (A): 58.39900 50.68000 48.72700 scale (grids/A): 0.6095995 object centre (A): 7.833501 1.331000 14.33550 number of atom coordinates read : 2550 total number of charged atoms : 2407 net assigned charge : -0.4999910 assigned positive charge : 384.5647 centred at (gu) : 91.42421 89.72696 89.72596 assigned negative charge : -385.0655 centred at (gu) : 91.34546 89.82533 89.76309 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6521 nv = 96 ne = 84 npr = 49153 no. pairs analyzed = 49153 no. exposed pairs = 3525 no. arc points = 25099 no. surface atoms = 1184 nbur = 1366 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3244 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2470 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7849 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5164018E-09 -2.0436606E-09 midg,1,midg; midg,igrid,midg 4.6251416E-09 -4.8752500E-09 1,midg,midg; igrid,midg,midg -3.0594165E-09 4.7424602E-09 gauss-seidel spectral radius is 0.9860771 estimated iterations to convergence 69 setup time was (sec) 0.5100000 now iterating at: 14:46:24 rms-change max change #iterations 0.1123705 18.30336 at 10iterations 1.0214593E-02 1.579193 at 20iterations 9.5893157E-04 0.1414804 at 30iterations 1.1637337E-04 2.4421692E-02 at 40iterations 1.9942487E-05 4.1732788E-03 at 50iterations finished qdiffx linear iterations at : 14:46:27 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.9942487E-05 4.1732788E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 14:46:27 3.107u 0.139s 0:03.52 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 Sun Oct 9 2011 at 14:46:27 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 1.828798 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): -21.36600 37.03300 ymin,ymax (A): -24.00900 26.67100 zmin,zma (A): -10.02800 38.69900 x,y,z range (A): 58.39900 50.68000 48.72700 scale (grids/A): 1.828798 object centre (A): 7.833501 1.331000 14.33550 number of atom coordinates read : 2550 total number of charged atoms : 2407 net assigned charge : -0.4999910 assigned positive charge : 384.5647 centred at (gu) : 94.27211 89.18027 89.17722 assigned negative charge : -385.0655 centred at (gu) : 94.03606 89.47584 89.28893 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25099 grid for indexing accessible points = 1.400000 m= 23181 mr = 46394 m= 3087 mr = 15825 m= 190 mr = 1647 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 319 time to turn everything in is 0.4800000 number of dielectric boundary points 33010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 18814 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) : 0.6095995 object centre at (A) : 7.833501 1.331000 14.33550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1789974E-02 -2.2830795E-03 midg,1,midg; midg,igrid,midg 3.9410973E-03 -1.9651551E-02 1,midg,midg; igrid,midg,midg -3.3464368E-02 2.8010530E-02 gauss-seidel spectral radius is 0.9985327 estimated iterations to convergence 207 setup time was (sec) 0.7500000 now iterating at: 14:46:28 rms-change max change #iterations 3.899311 174.6745 at 10iterations 1.762761 75.33311 at 20iterations 0.8028018 30.29598 at 30iterations 0.3619562 13.00508 at 40iterations 0.1650250 5.413542 at 50iterations 7.5023778E-02 2.343410 at 60iterations 3.4050737E-02 1.119911 at 70iterations 1.5467379E-02 0.6041374 at 80iterations 7.0615415E-03 0.2466507 at 90iterations 3.2088629E-03 0.1085949 at 100iterations 1.4711049E-03 4.8873901E-02 at 110iterations 6.7722646E-04 2.2521973E-02 at 120iterations finished qdiffx linear iterations at : 14:46:34 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 6.7722646E-04 2.2521973E-02 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 14:46:35 6.865u 0.157s 0:07.32 95.7% 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 Sun Oct 9 2011 at 14:46:35 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 2.743197 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): -21.36600 37.03300 ymin,ymax (A): -24.00900 26.67100 zmin,zma (A): -10.02800 38.69900 x,y,z range (A): 58.39900 50.68000 48.72700 scale (grids/A): 2.743197 object centre (A): 7.833501 1.331000 14.33550 number of atom coordinates read : 2550 total number of charged atoms : 2407 net assigned charge : -0.4999910 assigned positive charge : 384.5647 centred at (gu) : 96.40808 88.77010 88.76567 assigned negative charge : -385.0655 centred at (gu) : 96.05408 89.21367 88.93341 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 163272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25099 grid for indexing accessible points = 1.400000 m= 76560 mr = 113530 m= 24711 mr = 60129 m= 5084 mr = 18459 m= 721 mr = 3455 m= 51 mr = 425 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1099 time to turn everything in is 1.180000 number of dielectric boundary points 74382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 19255 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) : 1.828798 object centre at (A) : 7.833501 1.331000 14.33550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1789694 1.0793098E-02 midg,1,midg; midg,igrid,midg 7.8126967E-02 -0.2998241 1,midg,midg; igrid,midg,midg -0.3521724 0.5119082 gauss-seidel spectral radius is 0.9992390 estimated iterations to convergence 286 setup time was (sec) 1.470000 now iterating at: 14:46:36 rms-change max change #iterations 9.559727 362.4886 at 10iterations 5.637048 140.9963 at 20iterations 3.279449 67.44736 at 30iterations 1.899329 42.40362 at 40iterations 1.093595 21.35577 at 50iterations 0.6279014 13.42941 at 60iterations 0.3601523 8.058418 at 70iterations 0.2062509 3.953492 at 80iterations 0.1179256 2.279418 at 90iterations 6.7515798E-02 1.354765 at 100iterations 3.8488194E-02 0.7325249 at 110iterations 2.1955540E-02 0.3916469 at 120iterations 1.2561688E-02 0.2697678 at 130iterations 7.1882368E-03 0.1385822 at 140iterations 4.1238065E-03 8.7815285E-02 at 150iterations 2.3751929E-03 4.4269562E-02 at 160iterations 1.3703287E-03 2.9525757E-02 at 170iterations 7.9923542E-04 1.6475677E-02 at 180iterations finished qdiffx linear iterations at : 14:46:46 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 7.9923542E-04 1.6475677E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 14:46:47 11.789u 0.169s 0:12.24 97.5% 0+0k 0+0io 0pf+0w