Mon Oct 10 09:18:28 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 09:18:28 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5819277 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): 112.7790 173.9550 ymin,ymax (A): -45.46100 7.289000 zmin,zma (A): 49.31300 104.0340 x,y,z range (A): 61.17599 52.75000 54.72100 scale (grids/A): 0.5819277 object centre (A): 143.3670 -19.08600 76.67350 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : 6.014015 assigned positive charge : 422.0298 centred at (gu) : 89.96372 88.35677 89.07182 assigned negative charge : -416.0163 centred at (gu) : 89.95592 88.45487 88.91735 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6496 nv = 96 ne = 84 npr = 55184 no. pairs analyzed = 55184 no. exposed pairs = 4402 no. arc points = 31923 no. surface atoms = 1455 nbur = 1402 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 = 1.456000 m= 388 mr = 2776 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3147 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8161 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5701987E-09 3.8007042E-09 midg,1,midg; midg,igrid,midg 5.1827511E-09 -5.0569643E-10 1,midg,midg; igrid,midg,midg 1.2385204E-09 1.5570778E-09 gauss-seidel spectral radius is 0.9847677 estimated iterations to convergence 67 setup time was (sec) 0.5400000 now iterating at: 09:18:29 rms-change max change #iterations 9.8283648E-02 17.85671 at 10iterations 7.7396473E-03 1.283749 at 20iterations 6.0612225E-04 0.1063080 at 30iterations 4.7317775E-05 8.0308914E-03 at 40iterations 4.0442810E-06 6.4086914E-04 at 50iterations finished qdiffx linear iterations at : 09:18:31 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 4.0442810E-06 6.4086914E-04 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 09:18:32 3.148u 0.149s 0:03.64 90.1% 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 Mon Oct 10 2011 at 09:18:32 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.745783 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): 112.7790 173.9550 ymin,ymax (A): -45.46100 7.289000 zmin,zma (A): 49.31300 104.0340 x,y,z range (A): 61.17599 52.75000 54.72100 scale (grids/A): 1.745783 object centre (A): 143.3670 -19.08600 76.67350 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : 6.014015 assigned positive charge : 422.0298 centred at (gu) : 89.89061 85.06997 87.21507 assigned negative charge : -416.0163 centred at (gu) : 89.86762 85.36436 86.75194 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31923 grid for indexing accessible points = 1.400000 m= 23072 mr = 40632 m= 3684 mr = 14744 m= 192 mr = 1937 m= 0 mr = 18 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.5000000 number of dielectric boundary points 37858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 21004 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) : 0.5819277 object centre at (A) : 143.3670 -19.08600 76.67350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1179798E-02 2.9346390E-02 midg,1,midg; midg,igrid,midg 1.3398790E-02 3.3666396E-03 1,midg,midg; igrid,midg,midg 1.5834622E-02 5.2776682E-05 gauss-seidel spectral radius is 0.9984349 estimated iterations to convergence 201 setup time was (sec) 0.7700000 now iterating at: 09:18:33 rms-change max change #iterations 3.737672 161.7916 at 10iterations 1.653126 59.96909 at 20iterations 0.7330525 25.98513 at 30iterations 0.3236941 12.91737 at 40iterations 0.1428377 4.780508 at 50iterations 6.3054606E-02 2.241516 at 60iterations 2.7966561E-02 0.9916534 at 70iterations 1.2325829E-02 0.4649763 at 80iterations 5.4821363E-03 0.1817827 at 90iterations 2.4266385E-03 7.9326630E-02 at 100iterations 1.0743048E-03 3.5485029E-02 at 110iterations 4.7459203E-04 1.7213643E-02 at 120iterations finished qdiffx linear iterations at : 09:18:39 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 4.7459203E-04 1.7213643E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 09:18:40 7.122u 0.159s 0:07.71 94.2% 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 09:18:40 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.618675 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): 112.7790 173.9550 ymin,ymax (A): -45.46100 7.289000 zmin,zma (A): 49.31300 104.0340 x,y,z range (A): 61.17599 52.75000 54.72100 scale (grids/A): 2.618675 object centre (A): 143.3670 -19.08600 76.67350 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : 6.014015 assigned positive charge : 422.0298 centred at (gu) : 89.83601 82.60474 85.82237 assigned negative charge : -416.0163 centred at (gu) : 89.80134 83.04645 85.12783 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 157328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31923 grid for indexing accessible points = 1.400000 m= 72050 mr = 100304 m= 26819 mr = 53316 m= 6323 mr = 19764 m= 707 mr = 4180 m= 15 mr = 328 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 761 time to turn everything in is 1.230000 number of dielectric boundary points 85350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 21626 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) : 1.745783 object centre at (A) : 143.3670 -19.08600 76.67350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1677809 0.4010048 midg,1,midg; midg,igrid,midg 8.9315772E-02 9.4116956E-02 1,midg,midg; igrid,midg,midg 0.1692394 -0.1203553 gauss-seidel spectral radius is 0.9992365 estimated iterations to convergence 286 setup time was (sec) 1.540000 now iterating at: 09:18:42 rms-change max change #iterations 9.558525 361.8920 at 10iterations 5.676365 143.2471 at 20iterations 3.312764 75.72447 at 30iterations 1.923885 43.90526 at 40iterations 1.114681 24.71051 at 50iterations 0.6409160 15.05674 at 60iterations 0.3691025 8.485510 at 70iterations 0.2114689 4.388144 at 80iterations 0.1211447 2.473434 at 90iterations 6.9034666E-02 1.539862 at 100iterations 3.9530709E-02 0.8572025 at 110iterations 2.2550939E-02 0.4495335 at 120iterations 1.2838726E-02 0.2596912 at 130iterations 7.3294803E-03 0.1396503 at 140iterations 4.1742339E-03 8.1472397E-02 at 150iterations 2.3779441E-03 4.6215057E-02 at 160iterations 1.3542568E-03 2.6765823E-02 at 170iterations 7.6873956E-04 1.5967846E-02 at 180iterations finished qdiffx linear iterations at : 09:18:51 total time elapsed so far: 11.24000 # loops : 180 mean,max change (kT/e) : 7.6873956E-04 1.5967846E-02 energy calculations done at 11.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.40000 DelPhi exited at 09:18:52 11.406u 0.192s 0:11.90 97.3% 0+0k 0+0io 0pf+0w