Sun Oct 9 07:55:38 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+sph.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 = amb.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 Sun Oct 9 2011 at 07:55:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2163 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7150317 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): -16.22000 30.39100 ymin,ymax (A): -24.40400 25.38400 zmin,zma (A): -4.254000 35.01700 x,y,z range (A): 46.61100 49.78800 39.27100 scale (grids/A): 0.7150317 object centre (A): 7.085500 0.4899998 15.38150 number of atom coordinates read : 2163 total number of charged atoms : 2026 net assigned charge : 8.000017 assigned positive charge : 321.2596 centred at (gu) : 89.80722 90.35944 90.17885 assigned negative charge : -313.2599 centred at (gu) : 89.65240 90.39558 90.22671 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7389 nv = 96 ne = 84 npr = 44147 no. pairs analyzed = 44147 no. exposed pairs = 2810 no. arc points = 19867 no. surface atoms = 938 nbur = 1225 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 483 mr = 3976 m= 8 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 103 time to turn everything in is 0.1700000 number of dielectric boundary points 3825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1853 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0540066E-07 5.4545136E-08 midg,1,midg; midg,igrid,midg 9.5513471E-08 6.3804613E-08 1,midg,midg; igrid,midg,midg -1.1897555E-08 1.6438783E-07 gauss-seidel spectral radius is 0.9898159 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 07:55:39 rms-change max change #iterations 0.2063603 27.18963 at 10iterations 2.5891298E-02 3.308371 at 20iterations 3.2842455E-03 0.4514084 at 30iterations 4.1214086E-04 5.6018829E-02 at 40iterations 5.1265491E-05 7.1449280E-03 at 50iterations finished qdiffx linear iterations at : 07:55:42 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.1265491E-05 7.1449280E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 07:55:42 3.380u 0.167s 0:03.84 92.1% 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 Sun Oct 9 2011 at 07:55:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2163 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.145095 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): -16.22000 30.39100 ymin,ymax (A): -24.40400 25.38400 zmin,zma (A): -4.254000 35.01700 x,y,z range (A): 46.61100 49.78800 39.27100 scale (grids/A): 2.145095 object centre (A): 7.085500 0.4899998 15.38150 number of atom coordinates read : 2163 total number of charged atoms : 2026 net assigned charge : 8.000017 assigned positive charge : 321.2596 centred at (gu) : 89.42147 91.07776 90.53635 assigned negative charge : -313.2599 centred at (gu) : 88.95708 91.18638 90.67992 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19867 grid for indexing accessible points = 1.400000 m= 30411 mr = 53243 m= 5884 mr = 22690 m= 558 mr = 3797 m= 24 mr = 290 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2202 time to turn everything in is 0.3900000 number of dielectric boundary points 35213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16107 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) : 0.7150317 object centre at (A) : 7.085500 0.4899998 15.38150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1029194E-02 3.7042256E-02 midg,1,midg; midg,igrid,midg 3.5426773E-02 3.4437962E-02 1,midg,midg; igrid,midg,midg -1.5949778E-02 5.5678878E-02 gauss-seidel spectral radius is 0.9988679 estimated iterations to convergence 235 setup time was (sec) 0.6100000 now iterating at: 07:55:43 rms-change max change #iterations 4.713129 193.5771 at 10iterations 2.345394 75.32733 at 20iterations 1.169413 35.07690 at 30iterations 0.5870278 16.43493 at 40iterations 0.2938600 9.828691 at 50iterations 0.1465622 4.368095 at 60iterations 7.3410422E-02 2.123692 at 70iterations 3.6845844E-02 1.167549 at 80iterations 1.8392457E-02 0.5135970 at 90iterations 9.1962805E-03 0.2685333 at 100iterations 4.6208301E-03 0.1288619 at 110iterations 2.3139908E-03 6.7436218E-02 at 120iterations finished qdiffx linear iterations at : 07:55:50 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 2.3139908E-03 6.7436218E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 07:55:50 7.867u 0.192s 0:08.32 96.7% 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 Sun Oct 9 2011 at 07:55:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2163 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.217643 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): -16.22000 30.39100 ymin,ymax (A): -24.40400 25.38400 zmin,zma (A): -4.254000 35.01700 x,y,z range (A): 46.61100 49.78800 39.27100 scale (grids/A): 3.217643 object centre (A): 7.085500 0.4899998 15.38150 number of atom coordinates read : 2163 total number of charged atoms : 2026 net assigned charge : 8.000017 assigned positive charge : 321.2596 centred at (gu) : 89.13223 91.61671 90.80437 assigned negative charge : -313.2599 centred at (gu) : 88.43567 91.77946 91.01987 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 180559 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19867 grid for indexing accessible points = 1.400000 m= 94198 mr = 128805 m= 38575 mr = 77214 m= 11278 mr = 31544 m= 2293 mr = 8557 m= 321 mr = 1619 m= 27 mr = 227 m= 0 mr = 13 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 7083 time to turn everything in is 1.200000 number of dielectric boundary points 79272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 16208 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) : 2.145095 object centre at (A) : 7.085500 0.4899998 15.38150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6778497 0.3124855 midg,1,midg; midg,igrid,midg 0.2288250 0.3749751 1,midg,midg; igrid,midg,midg -7.1947075E-02 0.3954962 gauss-seidel spectral radius is 0.9993057 estimated iterations to convergence 299 setup time was (sec) 1.450000 now iterating at: 07:55:52 rms-change max change #iterations 10.40920 444.4183 at 10iterations 6.111179 124.7472 at 20iterations 3.576523 62.69560 at 30iterations 2.094821 39.95145 at 40iterations 1.226017 19.84012 at 50iterations 0.7156625 12.04097 at 60iterations 0.4185371 7.135300 at 70iterations 0.2450291 4.071260 at 80iterations 0.1429891 2.523708 at 90iterations 8.3460912E-02 1.702085 at 100iterations 4.8797011E-02 0.7931623 at 110iterations 2.8447332E-02 0.4686594 at 120iterations 1.6589014E-02 0.2678762 at 130iterations 9.6956734E-03 0.1675987 at 140iterations 5.6637009E-03 9.1339111E-02 at 150iterations 3.3052142E-03 5.4691315E-02 at 160iterations 1.9331734E-03 3.1602859E-02 at 170iterations 1.1300900E-03 2.0685196E-02 at 180iterations finished qdiffx linear iterations at : 07:56:04 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 1.1300900E-03 2.0685196E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 07:56:04 13.243u 0.201s 0:13.84 97.1% 0+0k 0+0io 0pf+0w