Sat Oct 8 11:34:16 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 Sat Oct 8 2011 at 11:34:17 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 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: 0.6698024 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): -94.86700 -46.47300 ymin,ymax (A): 54.71600 102.9660 zmin,zma (A): 76.60500 129.7550 x,y,z range (A): 48.39400 48.25000 53.15000 scale (grids/A): 0.6698024 object centre (A): -70.67000 78.84100 103.1800 number of atom coordinates read : 2379 total number of charged atoms : 2221 net assigned charge : -0.9999913 assigned positive charge : 345.7541 centred at (gu) : 88.65564 90.56188 88.27111 assigned negative charge : -346.7545 centred at (gu) : 88.69824 90.46593 88.22735 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7424 nv = 96 ne = 84 npr = 47948 no. pairs analyzed = 47948 no. exposed pairs = 3095 no. arc points = 21714 no. surface atoms = 1045 nbur = 1334 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 4040 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8420 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9032449E-08 4.4615338E-09 midg,1,midg; midg,igrid,midg -2.2416831E-08 2.0320764E-08 1,midg,midg; igrid,midg,midg 8.2978229E-09 -9.8673452E-09 gauss-seidel spectral radius is 0.9884337 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 11:34:17 rms-change max change #iterations 0.1726644 28.17896 at 10iterations 1.9295661E-02 2.899920 at 20iterations 2.1082342E-03 0.3123996 at 30iterations 2.3062581E-04 2.9683113E-02 at 40iterations 2.4841729E-05 3.2882690E-03 at 50iterations finished qdiffx linear iterations at : 11:34:21 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 2.4841729E-05 3.2882690E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.600000 DelPhi exited at 11:34:22 4.600u 0.255s 0:05.20 93.2% 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 Sat Oct 8 2011 at 11:34:22 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 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: 2.009407 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): -94.86700 -46.47300 ymin,ymax (A): 54.71600 102.9660 zmin,zma (A): 76.60500 129.7550 x,y,z range (A): 48.39400 48.25000 53.15000 scale (grids/A): 2.009407 object centre (A): -70.67000 78.84100 103.1800 number of atom coordinates read : 2379 total number of charged atoms : 2221 net assigned charge : -0.9999913 assigned positive charge : 345.7541 centred at (gu) : 85.96635 91.68513 84.81255 assigned negative charge : -346.7545 centred at (gu) : 86.09436 91.39749 84.68179 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21714 grid for indexing accessible points = 1.400000 m= 29191 mr = 54570 m= 4958 mr = 21526 m= 314 mr = 3184 m= 8 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 817 time to turn everything in is 0.4000000 number of dielectric boundary points 34417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17597 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) : 0.6698024 object centre at (A) : -70.67000 78.84100 103.1800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8954213E-03 3.2205008E-02 midg,1,midg; midg,igrid,midg -2.3784708E-02 -8.0614239E-03 1,midg,midg; igrid,midg,midg 2.6284851E-02 -1.1019501E-02 gauss-seidel spectral radius is 0.9987491 estimated iterations to convergence 224 setup time was (sec) 0.6700000 now iterating at: 11:34:23 rms-change max change #iterations 4.419292 197.9228 at 10iterations 2.131362 68.05861 at 20iterations 1.036537 31.26259 at 30iterations 0.4986913 14.57686 at 40iterations 0.2411929 7.647499 at 50iterations 0.1168814 3.472903 at 60iterations 5.6204565E-02 1.760933 at 70iterations 2.7321734E-02 0.8692665 at 80iterations 1.3208282E-02 0.3876543 at 90iterations 6.3841152E-03 0.1928110 at 100iterations 3.0846754E-03 9.2861176E-02 at 110iterations 1.4907037E-03 4.4902802E-02 at 120iterations finished qdiffx linear iterations at : 11:34:32 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 1.4907037E-03 4.4902802E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 11:34:32 9.525u 0.364s 0:10.22 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 Sat Oct 8 2011 at 11:34:32 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 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: 3.014111 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): -94.86700 -46.47300 ymin,ymax (A): 54.71600 102.9660 zmin,zma (A): 76.60500 129.7550 x,y,z range (A): 48.39400 48.25000 53.15000 scale (grids/A): 3.014111 object centre (A): -70.67000 78.84100 103.1800 number of atom coordinates read : 2379 total number of charged atoms : 2221 net assigned charge : -0.9999913 assigned positive charge : 345.7541 centred at (gu) : 83.94940 92.52759 82.21875 assigned negative charge : -346.7545 centred at (gu) : 84.14146 92.09615 82.02265 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 183777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21714 grid for indexing accessible points = 1.400000 m= 92348 mr = 132293 m= 35108 mr = 75537 m= 9194 mr = 28341 m= 1485 mr = 7044 m= 90 mr = 1064 m= 0 mr = 42 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 2743 time to turn everything in is 1.090000 number of dielectric boundary points 77681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 17768 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) : 2.009407 object centre at (A) : -70.67000 78.84100 103.1800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1658236E-03 0.2750541 midg,1,midg; midg,igrid,midg -0.2160870 -7.9008587E-02 1,midg,midg; igrid,midg,midg 0.2708762 -0.1480624 gauss-seidel spectral radius is 0.9992913 estimated iterations to convergence 296 setup time was (sec) 1.390000 now iterating at: 11:34:34 rms-change max change #iterations 10.27416 413.8373 at 10iterations 6.090042 147.4379 at 20iterations 3.591880 84.10664 at 30iterations 2.110522 39.89534 at 40iterations 1.237467 27.78127 at 50iterations 0.7250143 13.90115 at 60iterations 0.4241943 7.301964 at 70iterations 0.2476347 4.800315 at 80iterations 0.1446596 2.838563 at 90iterations 8.4267214E-02 1.520740 at 100iterations 4.9160168E-02 0.9169235 at 110iterations 2.8658180E-02 0.4677429 at 120iterations 1.6699223E-02 0.3089738 at 130iterations 9.6985176E-03 0.1743256 at 140iterations 5.6627071E-03 0.1038742 at 150iterations 3.2941892E-03 6.1923027E-02 at 160iterations 1.9182959E-03 3.2879829E-02 at 170iterations 1.1185430E-03 2.0211697E-02 at 180iterations finished qdiffx linear iterations at : 11:34:52 total time elapsed so far: 15.81000 # loops : 180 mean,max change (kT/e) : 1.1185430E-03 2.0211697E-02 energy calculations done at 15.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 11:34:52 15.946u 0.351s 0:20.33 80.1% 0+0k 0+0io 0pf+0w