Sat Oct 8 18:53:09 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 Sat Oct 8 2011 at 18:53:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 0.7106497 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): -28.65600 17.58800 ymin,ymax (A): -23.97000 23.27500 zmin,zma (A): -12.15100 37.94400 x,y,z range (A): 46.24400 47.24500 50.09500 scale (grids/A): 0.7106497 object centre (A): -5.534000 -0.3474998 12.89650 number of atom coordinates read : 2061 total number of charged atoms : 1924 net assigned charge : 4.500007 assigned positive charge : 303.0940 centred at (gu) : 89.34301 88.67370 90.06606 assigned negative charge : -298.5943 centred at (gu) : 89.24129 88.85132 89.86646 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7155 nv = 96 ne = 84 npr = 43294 no. pairs analyzed = 43294 no. exposed pairs = 2466 no. arc points = 17438 no. surface atoms = 822 nbur = 1239 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 508 mr = 4138 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2700000 number of dielectric boundary points 3439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1525 ## 123 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7878 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2400737E-08 1.4116648E-07 midg,1,midg; midg,igrid,midg 1.6694581E-07 -3.9265849E-08 1,midg,midg; igrid,midg,midg -1.4144303E-08 8.0308617E-08 gauss-seidel spectral radius is 0.9896808 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 18:53:10 rms-change max change #iterations 0.2068312 28.63429 at 10iterations 2.5573676E-02 4.142290 at 20iterations 3.1971291E-03 0.5057030 at 30iterations 3.9517923E-04 5.9310675E-02 at 40iterations 4.9218714E-05 6.9332123E-03 at 50iterations finished qdiffx linear iterations at : 18:53:14 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 4.9218714E-05 6.9332123E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 18:53:14 4.440u 0.415s 0:05.11 94.9% 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 Sat Oct 8 2011 at 18:53:14 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 2.131949 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): -28.65600 17.58800 ymin,ymax (A): -23.97000 23.27500 zmin,zma (A): -12.15100 37.94400 x,y,z range (A): 46.24400 47.24500 50.09500 scale (grids/A): 2.131949 object centre (A): -5.534000 -0.3474998 12.89650 number of atom coordinates read : 2061 total number of charged atoms : 1924 net assigned charge : 4.500007 assigned positive charge : 303.0940 centred at (gu) : 88.02921 86.02105 90.19804 assigned negative charge : -298.5943 centred at (gu) : 87.72408 86.55418 89.59955 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17438 grid for indexing accessible points = 1.400000 m= 29668 mr = 53666 m= 5897 mr = 22558 m= 605 mr = 3971 m= 18 mr = 262 m= 0 mr = 5 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1344 time to turn everything in is 0.6300000 number of dielectric boundary points 31664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15308 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) : 0.7106497 object centre at (A) : -5.534000 -0.3474998 12.89650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5880506E-02 2.0032441E-02 midg,1,midg; midg,igrid,midg 3.2119088E-02 1.8346757E-03 1,midg,midg; igrid,midg,midg 1.6469099E-02 7.5567126E-02 gauss-seidel spectral radius is 0.9988442 estimated iterations to convergence 233 setup time was (sec) 0.9700000 now iterating at: 18:53:16 rms-change max change #iterations 4.618658 220.7189 at 10iterations 2.294634 80.64604 at 20iterations 1.147658 35.42815 at 30iterations 0.5747135 17.84720 at 40iterations 0.2861205 9.103864 at 50iterations 0.1428779 4.267975 at 60iterations 7.1466856E-02 2.261856 at 70iterations 3.5472631E-02 1.062027 at 80iterations 1.7685322E-02 0.4913015 at 90iterations 8.8161966E-03 0.2666273 at 100iterations 4.3853205E-03 0.1244545 at 110iterations 2.1919394E-03 6.0688019E-02 at 120iterations finished qdiffx linear iterations at : 18:53:25 total time elapsed so far: 10.44000 # loops : 120 mean,max change (kT/e) : 2.1919394E-03 6.0688019E-02 energy calculations done at 10.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.61000 DelPhi exited at 18:53:26 10.614u 0.460s 0:11.33 97.7% 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 Sat Oct 8 2011 at 18:53:26 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 3.197924 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): -28.65600 17.58800 ymin,ymax (A): -23.97000 23.27500 zmin,zma (A): -12.15100 37.94400 x,y,z range (A): 46.24400 47.24500 50.09500 scale (grids/A): 3.197924 object centre (A): -5.534000 -0.3474998 12.89650 number of atom coordinates read : 2061 total number of charged atoms : 1924 net assigned charge : 4.500007 assigned positive charge : 303.0940 centred at (gu) : 87.04384 84.03165 90.29713 assigned negative charge : -298.5943 centred at (gu) : 86.58608 84.83131 89.39938 start vw surface at 0.1000000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 175270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17438 grid for indexing accessible points = 1.400000 m= 92445 mr = 128979 m= 37629 mr = 77333 m= 11316 mr = 31110 m= 2344 mr = 8670 m= 284 mr = 1650 m= 13 mr = 150 m= 0 mr = 2 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 4430 time to turn everything in is 1.940000 number of dielectric boundary points 71407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 15392 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) : 2.131949 object centre at (A) : -5.534000 -0.3474998 12.89650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1691654 0.1819233 midg,1,midg; midg,igrid,midg 0.2281907 2.3300909E-02 1,midg,midg; igrid,midg,midg 2.0152673E-02 0.7211316 gauss-seidel spectral radius is 0.9993047 estimated iterations to convergence 299 setup time was (sec) 2.250000 now iterating at: 18:53:28 rms-change max change #iterations 10.06929 376.1218 at 10iterations 5.900618 123.2734 at 20iterations 3.456973 66.14524 at 30iterations 2.020574 38.97110 at 40iterations 1.184270 20.00069 at 50iterations 0.6904293 11.69528 at 60iterations 0.4043318 7.113694 at 70iterations 0.2367997 4.270645 at 80iterations 0.1381096 2.323669 at 90iterations 8.0541305E-02 1.503830 at 100iterations 4.7179770E-02 0.8099575 at 110iterations 2.7497374E-02 0.4623175 at 120iterations 1.6035039E-02 0.2681499 at 130iterations 9.4126584E-03 0.1638227 at 140iterations 5.4980004E-03 9.8782539E-02 at 150iterations 3.2217635E-03 5.3508759E-02 at 160iterations 1.8830405E-03 3.0303955E-02 at 170iterations 1.1016076E-03 1.8394470E-02 at 180iterations finished qdiffx linear iterations at : 18:53:44 total time elapsed so far: 18.10000 # loops : 180 mean,max change (kT/e) : 1.1016076E-03 1.8394470E-02 energy calculations done at 18.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.54000 DelPhi exited at 18:53:45 18.542u 0.489s 0:19.36 98.2% 0+0k 0+0io 0pf+0w