Mon Oct 10 13:55:35 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 13:55:35 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2846 !!! WARNING: HIT 218 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6085366 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): 7.623000 61.19500 ymin,ymax (A): -20.56900 37.93200 zmin,zma (A): 38.26400 86.82600 x,y,z range (A): 53.57200 58.50100 48.56200 scale (grids/A): 0.6085366 object centre (A): 34.40900 8.681501 62.54500 number of atom coordinates read : 2846 total number of charged atoms : 2696 net assigned charge : -2.485975 assigned positive charge : 439.0892 centred at (gu) : 88.94650 89.76212 91.07765 assigned negative charge : -441.5761 centred at (gu) : 89.11695 89.89430 90.86871 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6965 nv = 96 ne = 84 npr = 57824 no. pairs analyzed = 57824 no. exposed pairs = 3404 no. arc points = 24089 no. surface atoms = 1141 nbur = 1705 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3900 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.2100000 number of dielectric boundary points 3345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2453 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8710 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0312572E-08 1.1995661E-08 midg,1,midg; midg,igrid,midg 5.6785190E-09 -8.3944069E-09 1,midg,midg; igrid,midg,midg 9.4014876E-09 -8.6655980E-09 gauss-seidel spectral radius is 0.9860384 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 13:55:36 rms-change max change #iterations 0.1224342 19.97276 at 10iterations 1.0804796E-02 1.604147 at 20iterations 9.8128768E-04 0.1319008 at 30iterations 1.0329767E-04 1.9409180E-02 at 40iterations 2.3057841E-05 4.7731400E-03 at 50iterations finished qdiffx linear iterations at : 13:55:39 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.3057841E-05 4.7731400E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 13:55:39 3.407u 0.178s 0:04.05 88.1% 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 Mon Oct 10 2011 at 13:55:39 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2846 !!! WARNING: HIT 218 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.825610 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): 7.623000 61.19500 ymin,ymax (A): -20.56900 37.93200 zmin,zma (A): 38.26400 86.82600 x,y,z range (A): 53.57200 58.50100 48.56200 scale (grids/A): 1.825610 object centre (A): 34.40900 8.681501 62.54500 number of atom coordinates read : 2846 total number of charged atoms : 2696 net assigned charge : -2.485975 assigned positive charge : 439.0892 centred at (gu) : 86.83891 89.28557 93.23212 assigned negative charge : -441.5761 centred at (gu) : 87.35055 89.68262 92.60579 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24089 grid for indexing accessible points = 1.400000 m= 26182 mr = 53619 m= 3536 mr = 19269 m= 146 mr = 2147 m= 0 mr = 30 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1463 time to turn everything in is 0.4000000 number of dielectric boundary points 30953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 21070 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) : 0.6085366 object centre at (A) : 34.40900 8.681501 62.54500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3467011E-02 1.7813733E-02 midg,1,midg; midg,igrid,midg 7.3188648E-02 5.3626299E-04 1,midg,midg; igrid,midg,midg -1.7872417E-03 -2.9111862E-02 gauss-seidel spectral radius is 0.9985376 estimated iterations to convergence 207 setup time was (sec) 0.6100000 now iterating at: 13:55:40 rms-change max change #iterations 4.217148 157.8463 at 10iterations 1.918924 68.80656 at 20iterations 0.8774802 29.86102 at 30iterations 0.4019665 14.74011 at 40iterations 0.1833541 5.660767 at 50iterations 8.3982378E-02 2.710117 at 60iterations 3.8215391E-02 1.195753 at 70iterations 1.7492946E-02 0.5917339 at 80iterations 7.9790596E-03 0.2665138 at 90iterations 3.6532078E-03 0.1129093 at 100iterations 1.6700545E-03 5.4809570E-02 at 110iterations 7.6597917E-04 2.3590088E-02 at 120iterations finished qdiffx linear iterations at : 13:55:47 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 7.6597917E-04 2.3590088E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 13:55:48 7.849u 0.193s 0:08.55 93.9% 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 13:55:48 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2846 !!! WARNING: HIT 218 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.738415 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): 7.623000 61.19500 ymin,ymax (A): -20.56900 37.93200 zmin,zma (A): 38.26400 86.82600 x,y,z range (A): 53.57200 58.50100 48.56200 scale (grids/A): 2.738415 object centre (A): 34.40900 8.681501 62.54500 number of atom coordinates read : 2846 total number of charged atoms : 2696 net assigned charge : -2.485975 assigned positive charge : 439.0892 centred at (gu) : 85.25834 88.92830 94.84821 assigned negative charge : -441.5761 centred at (gu) : 86.02583 89.52374 93.90844 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 176717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24089 grid for indexing accessible points = 1.400000 m= 87688 mr = 130533 m= 29121 mr = 71815 m= 6131 mr = 23282 m= 688 mr = 4555 m= 23 mr = 414 m= 0 mr = 8 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 5081 time to turn everything in is 0.9300000 number of dielectric boundary points 69761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 21565 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) : 1.825610 object centre at (A) : 34.40900 8.681501 62.54500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6104724 0.1087796 midg,1,midg; midg,igrid,midg 0.8529651 -3.6034450E-02 1,midg,midg; igrid,midg,midg -7.4350402E-02 -0.2614337 gauss-seidel spectral radius is 0.9992368 estimated iterations to convergence 286 setup time was (sec) 1.160000 now iterating at: 13:55:49 rms-change max change #iterations 10.04727 283.8989 at 10iterations 5.830702 152.5409 at 20iterations 3.370751 65.82118 at 30iterations 1.937635 38.02845 at 40iterations 1.116019 22.83440 at 50iterations 0.6387376 11.78655 at 60iterations 0.3663261 8.581099 at 70iterations 0.2093187 3.632279 at 80iterations 0.1197373 2.244596 at 90iterations 6.8280466E-02 1.251974 at 100iterations 3.8973715E-02 0.7269402 at 110iterations 2.2220779E-02 0.3873048 at 120iterations 1.2680884E-02 0.2333131 at 130iterations 7.2312555E-03 0.1336384 at 140iterations 4.1232263E-03 7.4609756E-02 at 150iterations 2.3509727E-03 4.5431614E-02 at 160iterations 1.3384456E-03 2.5912523E-02 at 170iterations 7.6347042E-04 1.4065683E-02 at 180iterations finished qdiffx linear iterations at : 13:56:01 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 7.6347042E-04 1.4065683E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 13:56:01 12.628u 0.228s 0:13.23 97.0% 0+0k 0+0io 0pf+0w