Mon Oct 10 18:29:14 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 Mon Oct 10 2011 at 18:29:15 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: SEP 137 has a net charge of -0.4750 !!! WARNING: ZN4 401 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: 0.5687628 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): 16.98300 61.97700 ymin,ymax (A): -51.19000 11.40200 zmin,zma (A): -13.55000 47.52200 x,y,z range (A): 44.99400 62.59200 61.07200 scale (grids/A): 0.5687628 object centre (A): 39.48000 -19.89400 16.98600 number of atom coordinates read : 2732 total number of charged atoms : 2581 net assigned charge : 16.62502 assigned positive charge : 409.5836 centred at (gu) : 90.25117 89.18052 88.71440 assigned negative charge : -392.9594 centred at (gu) : 90.23809 89.26139 88.79574 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5855 nv = 96 ne = 84 npr = 54598 no. pairs analyzed = 54598 no. exposed pairs = 3582 no. arc points = 25621 no. surface atoms = 1208 nbur = 1524 mkacc time = 0.1000000 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= 260 mr = 2950 m= 0 mr = 13 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2605 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7497 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7127453E-09 9.9303810E-10 midg,1,midg; midg,igrid,midg 4.2115835E-09 1.1046583E-09 1,midg,midg; igrid,midg,midg 2.1087811E-09 2.7365181E-09 gauss-seidel spectral radius is 0.9840344 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 18:29:15 rms-change max change #iterations 8.5242480E-02 13.77242 at 10iterations 6.4320862E-03 1.146792 at 20iterations 5.5060530E-04 9.3074799E-02 at 30iterations 6.9232650E-05 1.4863014E-02 at 40iterations 1.2889802E-05 3.0174255E-03 at 50iterations finished qdiffx linear iterations at : 18:29:18 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.2889802E-05 3.0174255E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 18:29:19 3.438u 0.159s 0:03.96 90.4% 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 Mon Oct 10 2011 at 18:29:19 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: SEP 137 has a net charge of -0.4750 !!! WARNING: ZN4 401 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: 1.706288 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): 16.98300 61.97700 ymin,ymax (A): -51.19000 11.40200 zmin,zma (A): -13.55000 47.52200 x,y,z range (A): 44.99400 62.59200 61.07200 scale (grids/A): 1.706288 object centre (A): 39.48000 -19.89400 16.98600 number of atom coordinates read : 2732 total number of charged atoms : 2581 net assigned charge : 16.62502 assigned positive charge : 409.5836 centred at (gu) : 90.75270 87.54048 86.14243 assigned negative charge : -392.9594 centred at (gu) : 90.71399 87.78400 86.38692 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64055 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25621 grid for indexing accessible points = 1.400000 m= 20453 mr = 42486 m= 2330 mr = 14027 m= 77 mr = 1159 m= 0 mr = 10 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1417 time to turn everything in is 0.3300000 number of dielectric boundary points 29233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19993 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) : 0.5687628 object centre at (A) : 39.48000 -19.89400 16.98600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9411517E-02 1.4568616E-02 midg,1,midg; midg,igrid,midg 4.7040950E-03 1.7389076E-02 1,midg,midg; igrid,midg,midg 1.2949747E-02 1.7151963E-02 gauss-seidel spectral radius is 0.9983189 estimated iterations to convergence 194 setup time was (sec) 0.5400000 now iterating at: 18:29:19 rms-change max change #iterations 3.428277 175.1323 at 10iterations 1.469367 54.67422 at 20iterations 0.6329513 22.73066 at 30iterations 0.2709096 9.993475 at 40iterations 0.1164789 4.111092 at 50iterations 5.0216481E-02 1.848034 at 60iterations 2.1595277E-02 0.7627592 at 70iterations 9.2889657E-03 0.3200054 at 80iterations 4.0159845E-03 0.1346684 at 90iterations 1.7446667E-03 6.7615509E-02 at 100iterations 7.5679284E-04 2.7565002E-02 at 110iterations 3.2980388E-04 1.1701584E-02 at 120iterations finished qdiffx linear iterations at : 18:29:26 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 3.2980388E-04 1.1701584E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 18:29:27 7.800u 0.199s 0:08.41 95.0% 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 Mon Oct 10 2011 at 18:29:27 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: SEP 137 has a net charge of -0.4750 !!! WARNING: ZN4 401 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: 2.559433 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): 16.98300 61.97700 ymin,ymax (A): -51.19000 11.40200 zmin,zma (A): -13.55000 47.52200 x,y,z range (A): 44.99400 62.59200 61.07200 scale (grids/A): 2.559433 object centre (A): 39.48000 -19.89400 16.98600 number of atom coordinates read : 2732 total number of charged atoms : 2581 net assigned charge : 16.62502 assigned positive charge : 409.5836 centred at (gu) : 91.12885 86.31063 84.21342 assigned negative charge : -392.9594 centred at (gu) : 91.07079 86.67603 84.58038 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 148580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25621 grid for indexing accessible points = 1.400000 m= 69622 mr = 104341 m= 20760 mr = 54877 m= 3747 mr = 15381 m= 312 mr = 2450 m= 12 mr = 143 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 4970 time to turn everything in is 0.7900000 number of dielectric boundary points 65839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20634 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) : 1.706288 object centre at (A) : 39.48000 -19.89400 16.98600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8161197 0.2513659 midg,1,midg; midg,igrid,midg 1.9294593E-02 0.3821819 1,midg,midg; igrid,midg,midg 0.1684976 0.2053609 gauss-seidel spectral radius is 0.9991733 estimated iterations to convergence 275 setup time was (sec) 1.020000 now iterating at: 18:29:28 rms-change max change #iterations 8.785877 293.4857 at 10iterations 5.049688 136.7329 at 20iterations 2.868474 76.77144 at 30iterations 1.622112 34.96023 at 40iterations 0.9119964 19.74529 at 50iterations 0.5121421 11.17176 at 60iterations 0.2864333 6.301626 at 70iterations 0.1599577 3.561342 at 80iterations 8.9318238E-02 2.153179 at 90iterations 4.9830213E-02 1.097576 at 100iterations 2.7783899E-02 0.5889053 at 110iterations 1.5447515E-02 0.3068743 at 120iterations 8.6227236E-03 0.1798983 at 130iterations 4.7947359E-03 0.1011658 at 140iterations 2.6751095E-03 6.2862396E-02 at 150iterations 1.4888432E-03 3.1012535E-02 at 160iterations 8.2847732E-04 1.5983582E-02 at 170iterations 4.6181385E-04 1.0056973E-02 at 180iterations finished qdiffx linear iterations at : 18:29:40 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 4.6181385E-04 1.0056973E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 18:29:40 12.506u 0.215s 0:13.06 97.3% 0+0k 0+0io 0pf+0w