Sat Oct 15 14:28:38 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 15 2011 at 14:28:38 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3193 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 0.5855552 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): -25.46700 32.33000 ymin,ymax (A): -8.966001 43.66600 zmin,zma (A): 6.851000 67.64800 x,y,z range (A): 57.79700 52.63200 60.79700 scale (grids/A): 0.5855552 object centre (A): 3.431499 17.35000 37.24950 number of atom coordinates read : 3193 total number of charged atoms : 3050 net assigned charge : -5.257958 assigned positive charge : 481.9315 centred at (gu) : 90.26421 88.61206 91.10616 assigned negative charge : -487.1909 centred at (gu) : 90.33736 88.46262 91.20443 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7232 nv = 96 ne = 84 npr = 63612 no. pairs analyzed = 63612 no. exposed pairs = 4145 no. arc points = 29163 no. surface atoms = 1401 nbur = 1792 mkacc time = 0.1100000 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 = 1.484000 m= 341 mr = 3762 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.2300000 number of dielectric boundary points 3790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2970 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1653501E-09 -5.3627449E-09 midg,1,midg; midg,igrid,midg -7.8485876E-09 2.1237467E-09 1,midg,midg; igrid,midg,midg 7.6507861E-10 -3.6146981E-09 gauss-seidel spectral radius is 0.9849668 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 14:28:39 rms-change max change #iterations 0.1063100 16.20407 at 10iterations 8.6173108E-03 1.476177 at 20iterations 6.9326803E-04 0.1003075 at 30iterations 6.4206142E-05 1.0354996E-02 at 40iterations 9.2716655E-06 2.0208359E-03 at 50iterations finished qdiffx linear iterations at : 14:28:44 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 9.2716655E-06 2.0208359E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 14:28:44 3.540u 0.203s 0:05.98 62.5% 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 Sat Oct 15 2011 at 14:28:45 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3193 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 1.756666 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): -25.46700 32.33000 ymin,ymax (A): -8.966001 43.66600 zmin,zma (A): 6.851000 67.64800 x,y,z range (A): 57.79700 52.63200 60.79700 scale (grids/A): 1.756666 object centre (A): 3.431499 17.35000 37.24950 number of atom coordinates read : 3193 total number of charged atoms : 3050 net assigned charge : -5.257958 assigned positive charge : 481.9315 centred at (gu) : 90.79121 85.83536 93.31734 assigned negative charge : -487.1909 centred at (gu) : 91.01165 85.38744 93.61298 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29163 grid for indexing accessible points = 1.400000 m= 25694 mr = 54054 m= 2949 mr = 17749 m= 109 mr = 1558 m= 4 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1211 time to turn everything in is 0.3800000 number of dielectric boundary points 35126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23786 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) : 0.5855552 object centre at (A) : 3.431499 17.35000 37.24950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9903913E-02 1.0087952E-02 midg,1,midg; midg,igrid,midg -4.8231158E-02 3.9286045E-03 1,midg,midg; igrid,midg,midg 1.5750377E-02 -3.5492174E-02 gauss-seidel spectral radius is 0.9984621 estimated iterations to convergence 202 setup time was (sec) 0.6100000 now iterating at: 14:28:45 rms-change max change #iterations 4.099865 201.3382 at 10iterations 1.816630 67.59306 at 20iterations 0.8121100 28.13671 at 30iterations 0.3613233 12.76819 at 40iterations 0.1610809 5.400990 at 50iterations 7.2197035E-02 2.171745 at 60iterations 3.2226421E-02 1.113119 at 70iterations 1.4391551E-02 0.4364414 at 80iterations 6.4489758E-03 0.2007790 at 90iterations 2.8805595E-03 9.6010208E-02 at 100iterations 1.2875716E-03 4.3052673E-02 at 110iterations 5.7694374E-04 1.7702103E-02 at 120iterations finished qdiffx linear iterations at : 14:28:59 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 5.7694374E-04 1.7702103E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 14:29:00 8.118u 0.237s 0:15.68 53.1% 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 15 2011 at 14:29:00 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3193 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 2.634998 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): -25.46700 32.33000 ymin,ymax (A): -8.966001 43.66600 zmin,zma (A): 6.851000 67.64800 x,y,z range (A): 57.79700 52.63200 60.79700 scale (grids/A): 2.634998 object centre (A): 3.431499 17.35000 37.24950 number of atom coordinates read : 3193 total number of charged atoms : 3050 net assigned charge : -5.257958 assigned positive charge : 481.9315 centred at (gu) : 91.18649 83.75296 94.97577 assigned negative charge : -487.1909 centred at (gu) : 91.51733 83.08102 95.41930 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 184761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29163 grid for indexing accessible points = 1.400000 m= 87168 mr = 131927 m= 26500 mr = 68860 m= 4864 mr = 20054 m= 509 mr = 3281 m= 15 mr = 305 m= 0 mr = 5 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 4356 time to turn everything in is 0.9700000 number of dielectric boundary points 79385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 24394 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) : 1.756666 object centre at (A) : 3.431499 17.35000 37.24950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6524976 0.2146759 midg,1,midg; midg,igrid,midg -0.6082263 5.7478391E-02 1,midg,midg; igrid,midg,midg 0.3432496 -0.3983034 gauss-seidel spectral radius is 0.9992328 estimated iterations to convergence 285 setup time was (sec) 1.220000 now iterating at: 14:29:02 rms-change max change #iterations 10.22886 263.7220 at 10iterations 5.974028 159.1367 at 20iterations 3.457579 80.50547 at 30iterations 1.995255 41.24516 at 40iterations 1.148378 22.36661 at 50iterations 0.6586857 15.70204 at 60iterations 0.3769417 8.174836 at 70iterations 0.2158028 4.460362 at 80iterations 0.1230236 2.362666 at 90iterations 7.0205905E-02 1.418652 at 100iterations 4.0027052E-02 0.7191229 at 110iterations 2.2786988E-02 0.4108477 at 120iterations 1.2983460E-02 0.2580649 at 130iterations 7.3903841E-03 0.1409950 at 140iterations 4.2146062E-03 8.1321716E-02 at 150iterations 2.4023871E-03 4.2579651E-02 at 160iterations 1.3673505E-03 2.4995804E-02 at 170iterations 7.7974115E-04 1.5365601E-02 at 180iterations finished qdiffx linear iterations at : 14:29:26 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 7.7974115E-04 1.5365601E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 14:29:27 13.339u 0.233s 0:26.32 51.5% 0+0k 0+0io 0pf+0w