Mon Oct 10 14:25:27 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 Mon Oct 10 2011 at 14:25:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2568 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: 0.5936401 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): -7.486000 44.07800 ymin,ymax (A): 13.16500 73.13400 zmin,zma (A): 55.12300 106.2750 x,y,z range (A): 51.56400 59.96899 51.15200 scale (grids/A): 0.5936401 object centre (A): 18.29600 43.14950 80.69901 number of atom coordinates read : 2568 total number of charged atoms : 2421 net assigned charge : -2.999997 assigned positive charge : 376.5670 centred at (gu) : 89.97388 90.48985 89.77406 assigned negative charge : -379.5674 centred at (gu) : 89.78381 90.43130 89.77722 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5998 nv = 96 ne = 84 npr = 51645 no. pairs analyzed = 51645 no. exposed pairs = 3510 no. arc points = 24208 no. surface atoms = 1182 nbur = 1386 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 279 mr = 3010 m= 0 mr = 10 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2378 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7449 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0006654E-09 -1.0814489E-09 midg,1,midg; midg,igrid,midg -2.4760547E-09 7.4345197E-10 1,midg,midg; igrid,midg,midg -6.7723205E-09 4.3683950E-09 gauss-seidel spectral radius is 0.9853178 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 14:25:28 rms-change max change #iterations 9.8889157E-02 17.14959 at 10iterations 8.1418939E-03 1.275955 at 20iterations 6.7876227E-04 0.1059856 at 30iterations 5.5589539E-05 8.4543228E-03 at 40iterations 4.7709732E-06 8.0871582E-04 at 50iterations finished qdiffx linear iterations at : 14:25:31 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 4.7709732E-06 8.0871582E-04 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 14:25:32 4.659u 0.399s 0:05.33 94.5% 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 14:25:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2568 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: 1.780920 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): -7.486000 44.07800 ymin,ymax (A): 13.16500 73.13400 zmin,zma (A): 55.12300 106.2750 x,y,z range (A): 51.56400 59.96899 51.15200 scale (grids/A): 1.780920 object centre (A): 18.29600 43.14950 80.69901 number of atom coordinates read : 2568 total number of charged atoms : 2421 net assigned charge : -2.999997 assigned positive charge : 376.5670 centred at (gu) : 89.92121 91.46915 89.32164 assigned negative charge : -379.5674 centred at (gu) : 89.35130 91.29348 89.33121 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65557 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24208 grid for indexing accessible points = 1.400000 m= 20508 mr = 43618 m= 2269 mr = 13832 m= 74 mr = 913 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.5400000 number of dielectric boundary points 30032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18885 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) : 0.5936401 object centre at (A) : 18.29600 43.14950 80.69901 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2615328E-02 1.9602207E-03 midg,1,midg; midg,igrid,midg -5.8125951E-03 -1.9398119E-02 1,midg,midg; igrid,midg,midg -2.5302062E-02 7.2973506E-03 gauss-seidel spectral radius is 0.9984426 estimated iterations to convergence 201 setup time was (sec) 0.8400000 now iterating at: 14:25:33 rms-change max change #iterations 3.643242 187.7409 at 10iterations 1.604880 57.91718 at 20iterations 0.7140062 28.25629 at 30iterations 0.3167928 11.27439 at 40iterations 0.1404595 4.585190 at 50iterations 6.2220208E-02 2.193114 at 60iterations 2.7768916E-02 0.9484742 at 70iterations 1.2374243E-02 0.4402111 at 80iterations 5.4897107E-03 0.2125168 at 90iterations 2.4431369E-03 9.4520569E-02 at 100iterations 1.0874768E-03 3.7447929E-02 at 110iterations 4.8435971E-04 1.6422272E-02 at 120iterations finished qdiffx linear iterations at : 14:25:44 total time elapsed so far: 11.16000 # loops : 120 mean,max change (kT/e) : 4.8435971E-04 1.6422272E-02 energy calculations done at 11.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.34000 DelPhi exited at 14:25:44 11.341u 0.474s 0:12.10 97.6% 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 Mon Oct 10 2011 at 14:25:44 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 = 2568 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: 2.671381 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): -7.486000 44.07800 ymin,ymax (A): 13.16500 73.13400 zmin,zma (A): 55.12300 106.2750 x,y,z range (A): 51.56400 59.96899 51.15200 scale (grids/A): 2.671381 object centre (A): 18.29600 43.14950 80.69901 number of atom coordinates read : 2568 total number of charged atoms : 2421 net assigned charge : -2.999997 assigned positive charge : 376.5670 centred at (gu) : 89.88165 92.20367 88.98251 assigned negative charge : -379.5674 centred at (gu) : 89.02676 91.94011 88.99677 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 151983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24208 grid for indexing accessible points = 1.400000 m= 70250 mr = 106948 m= 20678 mr = 54690 m= 3275 mr = 15089 m= 268 mr = 1920 m= 13 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 1.390000 number of dielectric boundary points 67697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 19365 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) : 1.780920 object centre at (A) : 18.29600 43.14950 80.69901 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2385190 2.6903886E-02 midg,1,midg; midg,igrid,midg -6.5347053E-02 -0.2909237 1,midg,midg; igrid,midg,midg -0.3186498 4.3702856E-02 gauss-seidel spectral radius is 0.9992111 estimated iterations to convergence 281 setup time was (sec) 1.750000 now iterating at: 14:25:46 rms-change max change #iterations 8.979745 337.7659 at 10iterations 5.228181 128.0927 at 20iterations 2.992498 73.01741 at 30iterations 1.715800 44.80548 at 40iterations 0.9782392 23.63333 at 50iterations 0.5565817 13.83115 at 60iterations 0.3156406 7.249630 at 70iterations 0.1792637 3.840144 at 80iterations 0.1014160 2.064886 at 90iterations 5.7373550E-02 1.197854 at 100iterations 3.2451551E-02 0.7583656 at 110iterations 1.8403349E-02 0.4066153 at 120iterations 1.0371144E-02 0.2154348 at 130iterations 5.8553014E-03 0.1170928 at 140iterations 3.3104140E-03 7.2567940E-02 at 150iterations 1.8683964E-03 4.1715622E-02 at 160iterations 1.0516951E-03 2.2844315E-02 at 170iterations 5.9554365E-04 1.2555122E-02 at 180iterations finished qdiffx linear iterations at : 14:26:03 total time elapsed so far: 18.42000 # loops : 180 mean,max change (kT/e) : 5.9554365E-04 1.2555122E-02 energy calculations done at 18.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.60000 DelPhi exited at 14:26:04 18.606u 0.512s 0:20.14 94.8% 0+0k 0+0io 0pf+0w