Mon Oct 10 09:47:20 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 09:47:20 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2863 !!! WARNING: HIT 233 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: 0.5893649 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): -17.98300 36.04600 ymin,ymax (A): -63.42000 -4.516000 zmin,zma (A): -4.583000 55.82100 x,y,z range (A): 54.02900 58.90400 60.40400 scale (grids/A): 0.5893649 object centre (A): 9.031499 -33.96800 25.61900 number of atom coordinates read : 2863 total number of charged atoms : 2710 net assigned charge : 4.014019 assigned positive charge : 419.8639 centred at (gu) : 89.62012 88.99673 87.99456 assigned negative charge : -415.8503 centred at (gu) : 89.82929 88.88618 87.84663 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6888 nv = 96 ne = 84 npr = 55227 no. pairs analyzed = 55227 no. exposed pairs = 4347 no. arc points = 31612 no. surface atoms = 1434 nbur = 1429 mkacc time = 0.1300000 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= 329 mr = 3060 m= 2 mr = 12 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 0.3200000 number of dielectric boundary points 4147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3062 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8432 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6635531E-09 3.3792085E-09 midg,1,midg; midg,igrid,midg -2.2925344E-09 3.4500292E-09 1,midg,midg; igrid,midg,midg 7.6305566E-09 -4.2358255E-09 gauss-seidel spectral radius is 0.9851491 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 09:47:21 rms-change max change #iterations 0.1000836 17.25367 at 10iterations 8.1161251E-03 1.318184 at 20iterations 7.0800824E-04 0.1252422 at 30iterations 7.5154938E-05 1.4663696E-02 at 40iterations 1.1823764E-05 2.3155212E-03 at 50iterations finished qdiffx linear iterations at : 09:47:23 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.1823764E-05 2.3155212E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 09:47:24 3.336u 0.133s 0:03.85 89.8% 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 09:47:24 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2863 !!! WARNING: HIT 233 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: 1.768095 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): -17.98300 36.04600 ymin,ymax (A): -63.42000 -4.516000 zmin,zma (A): -4.583000 55.82100 x,y,z range (A): 54.02900 58.90400 60.40400 scale (grids/A): 1.768095 object centre (A): 9.031499 -33.96800 25.61900 number of atom coordinates read : 2863 total number of charged atoms : 2710 net assigned charge : 4.014019 assigned positive charge : 419.8639 centred at (gu) : 88.85980 86.98991 83.98314 assigned negative charge : -415.8503 centred at (gu) : 89.48759 86.65833 83.53967 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31612 grid for indexing accessible points = 1.400000 m= 24472 mr = 45103 m= 3583 mr = 16028 m= 185 mr = 1799 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 38448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 21074 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) : 0.5893649 object centre at (A) : 9.031499 -33.96800 25.61900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8160924E-03 7.5891726E-03 midg,1,midg; midg,igrid,midg 2.3679988E-02 3.4667008E-02 1,midg,midg; igrid,midg,midg 1.8821619E-02 6.1052828E-03 gauss-seidel spectral radius is 0.9984724 estimated iterations to convergence 203 setup time was (sec) 0.8500000 now iterating at: 09:47:25 rms-change max change #iterations 3.863931 170.7880 at 10iterations 1.708126 58.39470 at 20iterations 0.7676774 28.47373 at 30iterations 0.3423255 11.14971 at 40iterations 0.1527984 5.612436 at 50iterations 6.8368115E-02 2.424889 at 60iterations 3.0530071E-02 1.010727 at 70iterations 1.3629229E-02 0.4933304 at 80iterations 6.0801753E-03 0.2068642 at 90iterations 2.7244852E-03 0.1030111 at 100iterations 1.2176696E-03 4.1870117E-02 at 110iterations 5.4653973E-04 1.7699242E-02 at 120iterations finished qdiffx linear iterations at : 09:47:31 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 5.4653973E-04 1.7699242E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 09:47:32 7.450u 0.151s 0:07.92 95.9% 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 Mon Oct 10 2011 at 09:47:32 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2863 !!! WARNING: HIT 233 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: 2.652142 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): -17.98300 36.04600 ymin,ymax (A): -63.42000 -4.516000 zmin,zma (A): -4.583000 55.82100 x,y,z range (A): 54.02900 58.90400 60.40400 scale (grids/A): 2.652142 object centre (A): 9.031499 -33.96800 25.61900 number of atom coordinates read : 2863 total number of charged atoms : 2710 net assigned charge : 4.014019 assigned positive charge : 419.8639 centred at (gu) : 88.28954 85.48467 80.97454 assigned negative charge : -415.8503 centred at (gu) : 89.23122 84.98740 80.30951 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 168757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31612 grid for indexing accessible points = 1.400000 m= 79104 mr = 111184 m= 27271 mr = 59578 m= 5979 mr = 19993 m= 723 mr = 3904 m= 22 mr = 366 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 86832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 21672 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) : 1.768095 object centre at (A) : 9.031499 -33.96800 25.61900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1183802 5.3804372E-02 midg,1,midg; midg,igrid,midg 0.6258937 0.5053290 1,midg,midg; igrid,midg,midg 0.1723639 0.1418782 gauss-seidel spectral radius is 0.9992422 estimated iterations to convergence 287 setup time was (sec) 1.680000 now iterating at: 09:47:34 rms-change max change #iterations 9.703359 258.5389 at 10iterations 5.724020 127.9263 at 20iterations 3.356297 79.13507 at 30iterations 1.947738 40.92348 at 40iterations 1.127564 24.91507 at 50iterations 0.6518463 13.36151 at 60iterations 0.3744159 8.095505 at 70iterations 0.2148353 4.863400 at 80iterations 0.1230416 2.791494 at 90iterations 7.0573144E-02 1.401085 at 100iterations 4.0361393E-02 0.7760329 at 110iterations 2.3037586E-02 0.5231705 at 120iterations 1.3184930E-02 0.2598343 at 130iterations 7.5213551E-03 0.1475444 at 140iterations 4.3005184E-03 8.9210510E-02 at 150iterations 2.4552061E-03 5.0289154E-02 at 160iterations 1.4046226E-03 2.9084444E-02 at 170iterations 8.0316345E-04 1.4739990E-02 at 180iterations finished qdiffx linear iterations at : 09:47:44 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 8.0316345E-04 1.4739990E-02 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 09:47:45 12.100u 0.185s 0:12.63 97.2% 0+0k 0+0io 0pf+0w