Tue Oct 11 00:47:17 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 Tue Oct 11 2011 at 00:47:17 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5669602 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): 18.11700 80.90800 ymin,ymax (A): -11.94300 44.14800 zmin,zma (A): -7.633000 35.18700 x,y,z range (A): 62.79100 56.09100 42.82000 scale (grids/A): 0.5669602 object centre (A): 49.51250 16.10250 13.77700 number of atom coordinates read : 2701 total number of charged atoms : 2550 net assigned charge : 6.312017 assigned positive charge : 409.3456 centred at (gu) : 87.57941 89.93249 89.85764 assigned negative charge : -403.0344 centred at (gu) : 87.77233 90.04402 89.98392 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5633 nv = 96 ne = 84 npr = 54060 no. pairs analyzed = 54060 no. exposed pairs = 3261 no. arc points = 23199 no. surface atoms = 1098 nbur = 1603 mkacc time = 0.1200000 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 = 1.512000 m= 231 mr = 3077 m= 0 mr = 13 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.2900000 number of dielectric boundary points 2774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2304 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7256 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4639388E-09 -8.0993506E-10 midg,1,midg; midg,igrid,midg 2.2345492E-09 -6.3522071E-10 1,midg,midg; igrid,midg,midg 5.7694942E-09 -9.4997410E-10 gauss-seidel spectral radius is 0.9839231 estimated iterations to convergence 65 setup time was (sec) 0.5100000 now iterating at: 00:47:18 rms-change max change #iterations 8.7360598E-02 14.61494 at 10iterations 7.3768622E-03 1.200909 at 20iterations 9.2687370E-04 0.2371750 at 30iterations 1.9483750E-04 5.1403046E-02 at 40iterations 4.2973687E-05 1.1669159E-02 at 50iterations finished qdiffx linear iterations at : 00:47:21 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 4.2973687E-05 1.1669159E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 00:47:21 3.261u 0.187s 0:03.98 86.4% 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 Tue Oct 11 2011 at 00:47:21 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.700881 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): 18.11700 80.90800 ymin,ymax (A): -11.94300 44.14800 zmin,zma (A): -7.633000 35.18700 x,y,z range (A): 62.79100 56.09100 42.82000 scale (grids/A): 1.700881 object centre (A): 49.51250 16.10250 13.77700 number of atom coordinates read : 2701 total number of charged atoms : 2550 net assigned charge : 6.312017 assigned positive charge : 409.3456 centred at (gu) : 82.73782 89.79678 89.57233 assigned negative charge : -403.0344 centred at (gu) : 83.31664 90.13174 89.95145 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62658 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23199 grid for indexing accessible points = 1.400000 m= 19368 mr = 43336 m= 2175 mr = 13822 m= 70 mr = 1197 m= 0 mr = 7 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2236 time to turn everything in is 0.4700000 number of dielectric boundary points 25909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19661 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) : 0.5669602 object centre at (A) : 49.51250 16.10250 13.77700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4943704E-02 1.9667647E-03 midg,1,midg; midg,igrid,midg 1.5615304E-02 -1.6681455E-02 1,midg,midg; igrid,midg,midg -2.3976217E-03 5.7190075E-03 gauss-seidel spectral radius is 0.9982969 estimated iterations to convergence 192 setup time was (sec) 0.7500000 now iterating at: 00:47:22 rms-change max change #iterations 3.457003 157.1308 at 10iterations 1.473956 55.31789 at 20iterations 0.6308588 22.70425 at 30iterations 0.2705805 11.11868 at 40iterations 0.1165413 4.368778 at 50iterations 5.0161649E-02 1.751698 at 60iterations 2.1665141E-02 0.7677383 at 70iterations 9.3881022E-03 0.3335037 at 80iterations 4.1058166E-03 0.1503296 at 90iterations 1.8638244E-03 7.8674316E-02 at 100iterations 8.7411911E-04 4.0630341E-02 at 110iterations 4.3033750E-04 1.9874573E-02 at 120iterations finished qdiffx linear iterations at : 00:47:29 total time elapsed so far: 7.090000 # loops : 120 mean,max change (kT/e) : 4.3033750E-04 1.9874573E-02 energy calculations done at 7.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.260000 DelPhi exited at 00:47:29 7.261u 0.214s 0:07.90 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 Tue Oct 11 2011 at 00:47:29 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.551321 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): 18.11700 80.90800 ymin,ymax (A): -11.94300 44.14800 zmin,zma (A): -7.633000 35.18700 x,y,z range (A): 62.79100 56.09100 42.82000 scale (grids/A): 2.551321 object centre (A): 49.51250 16.10250 13.77700 number of atom coordinates read : 2701 total number of charged atoms : 2550 net assigned charge : 6.312017 assigned positive charge : 409.3456 centred at (gu) : 79.10651 89.69512 89.35831 assigned negative charge : -403.0344 centred at (gu) : 79.97500 90.19759 89.92711 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 145834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23199 grid for indexing accessible points = 1.400000 m= 67195 mr = 105850 m= 19765 mr = 54202 m= 3533 mr = 15439 m= 262 mr = 2547 m= 2 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 7704 time to turn everything in is 1.030000 number of dielectric boundary points 58427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20383 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) : 1.700881 object centre at (A) : 49.51250 16.10250 13.77700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1680296 2.2683250E-02 midg,1,midg; midg,igrid,midg 0.1715464 -0.3900656 1,midg,midg; igrid,midg,midg -8.1393443E-02 0.1710017 gauss-seidel spectral radius is 0.9991582 estimated iterations to convergence 272 setup time was (sec) 1.340000 now iterating at: 00:47:31 rms-change max change #iterations 8.532141 318.5876 at 10iterations 4.728395 124.0578 at 20iterations 2.630306 60.15314 at 30iterations 1.458893 31.97908 at 40iterations 0.8082762 16.66052 at 50iterations 0.4476084 9.315701 at 60iterations 0.2480297 5.231506 at 70iterations 0.1372015 3.106007 at 80iterations 7.5842977E-02 1.552127 at 90iterations 4.1975997E-02 0.8605652 at 100iterations 2.3225434E-02 0.4722481 at 110iterations 1.2931752E-02 0.2551003 at 120iterations 7.2212880E-03 0.1634350 at 130iterations 4.0773577E-03 8.4899902E-02 at 140iterations 2.3290215E-03 5.4952621E-02 at 150iterations 1.3641426E-03 3.3454895E-02 at 160iterations 8.3085935E-04 2.1713257E-02 at 170iterations 5.2420131E-04 1.5300751E-02 at 180iterations finished qdiffx linear iterations at : 00:47:41 total time elapsed so far: 11.31000 # loops : 180 mean,max change (kT/e) : 5.2420131E-04 1.5300751E-02 energy calculations done at 11.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 00:47:42 11.495u 0.214s 0:12.10 96.6% 0+0k 0+0io 0pf+0w