Sun Oct 9 22:34:15 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 Sun Oct 9 2011 at 22:34:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 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: 0.6317321 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): -2.710000 46.04500 ymin,ymax (A): -44.32200 8.059000 zmin,zma (A): -46.67100 9.681999 x,y,z range (A): 48.75500 52.38100 56.35300 scale (grids/A): 0.6317321 object centre (A): 21.66750 -18.13150 -18.49450 number of atom coordinates read : 2565 total number of charged atoms : 2429 net assigned charge : 5.000012 assigned positive charge : 387.9479 centred at (gu) : 91.14165 89.88047 89.48213 assigned negative charge : -382.9487 centred at (gu) : 91.09011 89.88638 89.44312 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6683 nv = 96 ne = 84 npr = 51893 no. pairs analyzed = 51893 no. exposed pairs = 3104 no. arc points = 22448 no. surface atoms = 1059 nbur = 1506 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3546 m= 0 mr = 32 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 76 time to turn everything in is 0.1800000 number of dielectric boundary points 3424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2303 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8252 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3048876E-09 8.2683087E-09 midg,1,midg; midg,igrid,midg 6.3755450E-09 5.0093010E-09 1,midg,midg; igrid,midg,midg 7.8583168E-10 1.3263846E-08 gauss-seidel spectral radius is 0.9870167 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 22:34:16 rms-change max change #iterations 0.1346945 20.92618 at 10iterations 1.2904440E-02 1.845917 at 20iterations 1.2328359E-03 0.1871185 at 30iterations 1.1739317E-04 1.6506195E-02 at 40iterations 1.1282457E-05 1.5239716E-03 at 50iterations finished qdiffx linear iterations at : 22:34:19 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.1282457E-05 1.5239716E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 22:34:19 3.424u 0.197s 0:03.88 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 Sun Oct 9 2011 at 22:34:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 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: 1.895196 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): -2.710000 46.04500 ymin,ymax (A): -44.32200 8.059000 zmin,zma (A): -46.67100 9.681999 x,y,z range (A): 48.75500 52.38100 56.35300 scale (grids/A): 1.895196 object centre (A): 21.66750 -18.13150 -18.49450 number of atom coordinates read : 2565 total number of charged atoms : 2429 net assigned charge : 5.000012 assigned positive charge : 387.9479 centred at (gu) : 93.42456 89.64075 88.44612 assigned negative charge : -382.9487 centred at (gu) : 93.27023 89.65919 88.32899 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22448 grid for indexing accessible points = 1.400000 m= 24179 mr = 49710 m= 3559 mr = 17401 m= 205 mr = 2141 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3281 time to turn everything in is 0.3700000 number of dielectric boundary points 31357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19068 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) : 0.6317321 object centre at (A) : 21.66750 -18.13150 -18.49450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6329634E-02 1.4090658E-02 midg,1,midg; midg,igrid,midg -9.0363948E-03 -2.3372142E-04 1,midg,midg; igrid,midg,midg -8.0168769E-03 1.4402600E-02 gauss-seidel spectral radius is 0.9986144 estimated iterations to convergence 213 setup time was (sec) 0.6000000 now iterating at: 22:34:20 rms-change max change #iterations 4.112999 204.4073 at 10iterations 1.905132 70.39484 at 20iterations 0.8864024 27.84808 at 30iterations 0.4137323 13.34236 at 40iterations 0.1916571 7.114410 at 50iterations 8.9340501E-02 2.906411 at 60iterations 4.1636754E-02 1.536852 at 70iterations 1.9373259E-02 0.6178589 at 80iterations 9.0074949E-03 0.2931359 at 90iterations 4.1943798E-03 0.1467180 at 100iterations 1.9500258E-03 6.7225933E-02 at 110iterations 9.0774434E-04 2.8641701E-02 at 120iterations finished qdiffx linear iterations at : 22:34:27 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 9.0774434E-04 2.8641701E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 22:34:28 7.954u 0.186s 0:08.41 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 Sun Oct 9 2011 at 22:34:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 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: 2.842794 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): -2.710000 46.04500 ymin,ymax (A): -44.32200 8.059000 zmin,zma (A): -46.67100 9.681999 x,y,z range (A): 48.75500 52.38100 56.35300 scale (grids/A): 2.842794 object centre (A): 21.66750 -18.13150 -18.49450 number of atom coordinates read : 2565 total number of charged atoms : 2429 net assigned charge : 5.000012 assigned positive charge : 387.9479 centred at (gu) : 95.13653 89.46102 87.66907 assigned negative charge : -382.9487 centred at (gu) : 94.90531 89.48885 87.49343 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22448 grid for indexing accessible points = 1.400000 m= 80470 mr = 120866 m= 26871 mr = 65050 m= 6454 mr = 21101 m= 947 mr = 4767 m= 54 mr = 628 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 10947 time to turn everything in is 0.9100000 number of dielectric boundary points 70689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19429 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) : 1.895196 object centre at (A) : 21.66750 -18.13150 -18.49450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3183332 0.2103037 midg,1,midg; midg,igrid,midg -0.2338301 8.4998451E-02 1,midg,midg; igrid,midg,midg -0.1643417 0.2106601 gauss-seidel spectral radius is 0.9992528 estimated iterations to convergence 289 setup time was (sec) 1.140000 now iterating at: 22:34:29 rms-change max change #iterations 9.644494 407.7535 at 10iterations 5.583780 149.2192 at 20iterations 3.223989 76.69058 at 30iterations 1.856053 37.87648 at 40iterations 1.064423 20.35176 at 50iterations 0.6105725 11.03291 at 60iterations 0.3500440 6.588238 at 70iterations 0.2004358 4.092295 at 80iterations 0.1147777 2.118010 at 90iterations 6.5595947E-02 1.158737 at 100iterations 3.7543532E-02 0.6683731 at 110iterations 2.1482162E-02 0.4070477 at 120iterations 1.2298223E-02 0.2348795 at 130iterations 7.0450073E-03 0.1312714 at 140iterations 4.0271077E-03 7.7926636E-02 at 150iterations 2.3070849E-03 5.0483704E-02 at 160iterations 1.3176297E-03 2.4360657E-02 at 170iterations 7.5521081E-04 1.3670921E-02 at 180iterations finished qdiffx linear iterations at : 22:34:41 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 7.5521081E-04 1.3670921E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 22:34:41 12.753u 0.229s 0:13.25 97.8% 0+0k 0+0io 0pf+0w