Sat Oct 8 23:28:42 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 23:28:42 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2348 !!! WARNING: HIT 84 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: 0.6522296 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): -1.129000 53.45300 ymin,ymax (A): 8.299000 51.45100 zmin,zma (A): -3.397000 48.82100 x,y,z range (A): 54.58200 43.15200 52.21800 scale (grids/A): 0.6522296 object centre (A): 26.16200 29.87500 22.71200 number of atom coordinates read : 2348 total number of charged atoms : 2213 net assigned charge : 11.01402 assigned positive charge : 345.4783 centred at (gu) : 90.00157 90.50615 88.43190 assigned negative charge : -334.4651 centred at (gu) : 89.97063 90.44980 88.41116 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6905 nv = 96 ne = 84 npr = 46942 no. pairs analyzed = 46942 no. exposed pairs = 3104 no. arc points = 22120 no. surface atoms = 1036 nbur = 1312 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 3653 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2182 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8110 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7074456E-08 1.8542888E-08 midg,1,midg; midg,igrid,midg 1.3315358E-08 3.3719907E-08 1,midg,midg; igrid,midg,midg 1.8264160E-08 2.6881896E-08 gauss-seidel spectral radius is 0.9878033 estimated iterations to convergence 74 setup time was (sec) 0.6100000 now iterating at: 23:28:43 rms-change max change #iterations 0.1515054 24.26464 at 10iterations 1.5570336E-02 2.177389 at 20iterations 1.7250411E-03 0.2763033 at 30iterations 2.7865643E-04 4.6894073E-02 at 40iterations 8.3225670E-05 1.6225815E-02 at 50iterations finished qdiffx linear iterations at : 23:28:46 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 8.3225670E-05 1.6225815E-02 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 23:28:47 4.062u 0.239s 0:04.56 94.0% 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 Sat Oct 8 2011 at 23:28:47 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2348 !!! WARNING: HIT 84 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: 1.956689 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): -1.129000 53.45300 ymin,ymax (A): 8.299000 51.45100 zmin,zma (A): -3.397000 48.82100 x,y,z range (A): 54.58200 43.15200 52.21800 scale (grids/A): 1.956689 object centre (A): 26.16200 29.87500 22.71200 number of atom coordinates read : 2348 total number of charged atoms : 2213 net assigned charge : 11.01402 assigned positive charge : 345.4783 centred at (gu) : 90.00420 91.51817 85.29539 assigned negative charge : -334.4651 centred at (gu) : 89.91207 91.34934 85.23354 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22120 grid for indexing accessible points = 1.400000 m= 27073 mr = 50118 m= 4652 mr = 19530 m= 331 mr = 2854 m= 5 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 33221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 17479 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) : 0.6522296 object centre at (A) : 26.16200 29.87500 22.71200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4668198E-02 4.1779671E-02 midg,1,midg; midg,igrid,midg 3.7569734E-03 2.8491782E-02 1,midg,midg; igrid,midg,midg 3.9717942E-02 5.7879046E-02 gauss-seidel spectral radius is 0.9986873 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 23:28:48 rms-change max change #iterations 4.131411 171.7144 at 10iterations 1.962873 67.95399 at 20iterations 0.9278037 32.85362 at 30iterations 0.4405812 16.47964 at 40iterations 0.2096423 6.401646 at 50iterations 9.9437073E-02 3.211670 at 60iterations 4.7121100E-02 1.663622 at 70iterations 2.2407925E-02 0.7933064 at 80iterations 1.0706373E-02 0.3421860 at 90iterations 5.1126513E-03 0.1740685 at 100iterations 2.4638069E-03 8.1281662E-02 at 110iterations 1.2157332E-03 4.3457031E-02 at 120iterations finished qdiffx linear iterations at : 23:28:56 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 1.2157332E-03 4.3457031E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.400000 DelPhi exited at 23:28:57 9.405u 0.292s 0:10.00 96.9% 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 23:28:57 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2348 !!! WARNING: HIT 84 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: 2.935033 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): -1.129000 53.45300 ymin,ymax (A): 8.299000 51.45100 zmin,zma (A): -3.397000 48.82100 x,y,z range (A): 54.58200 43.15200 52.21800 scale (grids/A): 2.935033 object centre (A): 26.16200 29.87500 22.71200 number of atom coordinates read : 2348 total number of charged atoms : 2213 net assigned charge : 11.01402 assigned positive charge : 345.4783 centred at (gu) : 90.00620 92.27703 82.94308 assigned negative charge : -334.4651 centred at (gu) : 89.86806 92.02396 82.85037 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 170383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22120 grid for indexing accessible points = 1.400000 m= 85935 mr = 121370 m= 32629 mr = 69361 m= 8591 mr = 25940 m= 1443 mr = 6334 m= 89 mr = 984 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 75040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 17704 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) : 1.956689 object centre at (A) : 26.16200 29.87500 22.71200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3007554 0.5300730 midg,1,midg; midg,igrid,midg 3.3376575E-03 0.2648684 1,midg,midg; igrid,midg,midg 0.3407483 0.5656794 gauss-seidel spectral radius is 0.9992747 estimated iterations to convergence 293 setup time was (sec) 2.070000 now iterating at: 23:28:59 rms-change max change #iterations 9.770039 360.1910 at 10iterations 5.778274 146.2227 at 20iterations 3.400249 77.80102 at 30iterations 1.986079 40.63744 at 40iterations 1.163360 27.13665 at 50iterations 0.6790780 13.26217 at 60iterations 0.3949045 7.959501 at 70iterations 0.2297433 4.658308 at 80iterations 0.1334324 2.545635 at 90iterations 7.7513069E-02 1.617575 at 100iterations 4.4830695E-02 0.8848877 at 110iterations 2.6032144E-02 0.5254941 at 120iterations 1.5087089E-02 0.3010101 at 130iterations 8.7379022E-03 0.1552544 at 140iterations 5.0720372E-03 9.1993332E-02 at 150iterations 2.9574444E-03 5.4164886E-02 at 160iterations 1.7288392E-03 3.2726765E-02 at 170iterations 1.0229608E-03 2.0709991E-02 at 180iterations finished qdiffx linear iterations at : 23:29:13 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 1.0229608E-03 2.0709991E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 23:29:13 15.864u 0.284s 0:16.41 98.3% 0+0k 0+0io 0pf+0w