Sun Oct 9 14:41:56 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 14:41:56 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 = 2961 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: 0.5332375 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): -31.04500 28.23300 ymin,ymax (A): -24.75400 42.00800 zmin,zma (A): -18.10500 39.48300 x,y,z range (A): 59.27800 66.76200 57.58800 scale (grids/A): 0.5332375 object centre (A): -1.406000 8.627002 10.68900 number of atom coordinates read : 2961 total number of charged atoms : 2818 net assigned charge : 6.500019 assigned positive charge : 444.7319 centred at (gu) : 90.38062 89.17408 89.00220 assigned negative charge : -438.2334 centred at (gu) : 90.37912 89.34297 89.04957 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5629 nv = 96 ne = 84 npr = 56189 no. pairs analyzed = 56189 no. exposed pairs = 4199 no. arc points = 30758 no. surface atoms = 1402 nbur = 1559 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 = 1.624000 m= 225 mr = 2496 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3170 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4505173E-10 3.5725922E-11 midg,1,midg; midg,igrid,midg 1.1095941E-09 -3.6929770E-10 1,midg,midg; igrid,midg,midg 2.0838863E-10 2.6434890E-10 gauss-seidel spectral radius is 0.9818946 estimated iterations to convergence 61 setup time was (sec) 0.5900000 now iterating at: 14:41:57 rms-change max change #iterations 6.0791362E-02 11.04056 at 10iterations 3.7744259E-03 0.7915421 at 20iterations 2.4673773E-04 4.6193123E-02 at 30iterations 1.9484214E-05 3.4408569E-03 at 40iterations 2.2514096E-06 3.5381317E-04 at 50iterations finished qdiffx linear iterations at : 14:42:00 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 2.2514096E-06 3.5381317E-04 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 14:42:01 4.203u 0.224s 0:04.71 93.8% 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 Sun Oct 9 2011 at 14:42:01 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 = 2961 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: 1.599712 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): -31.04500 28.23300 ymin,ymax (A): -24.75400 42.00800 zmin,zma (A): -18.10500 39.48300 x,y,z range (A): 59.27800 66.76200 57.58800 scale (grids/A): 1.599712 object centre (A): -1.406000 8.627002 10.68900 number of atom coordinates read : 2961 total number of charged atoms : 2818 net assigned charge : 6.500019 assigned positive charge : 444.7319 centred at (gu) : 91.14108 87.52119 87.00599 assigned negative charge : -438.2334 centred at (gu) : 91.13731 88.02871 87.14849 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 61103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30758 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 17171 mr = 37436 m= 1660 mr = 10707 m= 34 mr = 675 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 31147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 417 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 21435 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) : 0.5332375 object centre at (A) : -1.406000 8.627002 10.68900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8532490E-02 7.1128784E-03 midg,1,midg; midg,igrid,midg 2.3241462E-02 -6.6922489E-03 1,midg,midg; igrid,midg,midg 6.7109929E-04 -1.0114793E-02 gauss-seidel spectral radius is 0.9981250 estimated iterations to convergence 184 setup time was (sec) 0.9100000 now iterating at: 14:42:02 rms-change max change #iterations 3.149897 203.3441 at 10iterations 1.279260 50.90145 at 20iterations 0.5258422 22.40662 at 30iterations 0.2147241 8.525993 at 40iterations 8.7984234E-02 3.229805 at 50iterations 3.6070980E-02 1.392538 at 60iterations 1.4844224E-02 0.5054231 at 70iterations 6.0737999E-03 0.2311707 at 80iterations 2.4939415E-03 0.1007118 at 90iterations 1.0211015E-03 3.7122965E-02 at 100iterations 4.2045652E-04 1.5075684E-02 at 110iterations 1.7231150E-04 7.1052313E-03 at 120iterations finished qdiffx linear iterations at : 14:42:11 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 1.7231150E-04 7.1052313E-03 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 14:42:11 9.654u 0.267s 0:10.29 96.3% 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 14:42:11 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 = 2961 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: 2.399569 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): -31.04500 28.23300 ymin,ymax (A): -24.75400 42.00800 zmin,zma (A): -18.10500 39.48300 x,y,z range (A): 59.27800 66.76200 57.58800 scale (grids/A): 2.399569 object centre (A): -1.406000 8.627002 10.68900 number of atom coordinates read : 2961 total number of charged atoms : 2818 net assigned charge : 6.500019 assigned positive charge : 444.7319 centred at (gu) : 91.71140 86.28158 85.50883 assigned negative charge : -438.2334 centred at (gu) : 91.70592 87.04301 85.72256 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 141562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30758 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 60082 mr = 92629 m= 15684 mr = 44816 m= 2341 mr = 10833 m= 143 mr = 1427 m= 0 mr = 43 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 70064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 22495 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) : 1.599712 object centre at (A) : -1.406000 8.627002 10.68900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3208726 0.1682969 midg,1,midg; midg,igrid,midg 0.3578954 -9.1745436E-02 1,midg,midg; igrid,midg,midg 9.5124310E-03 -0.2367299 gauss-seidel spectral radius is 0.9991310 estimated iterations to convergence 268 setup time was (sec) 1.550000 now iterating at: 14:42:13 rms-change max change #iterations 8.427134 304.8524 at 10iterations 4.697032 134.1478 at 20iterations 2.629391 67.87721 at 30iterations 1.458266 35.83392 at 40iterations 0.8080735 24.36039 at 50iterations 0.4469954 10.08117 at 60iterations 0.2456567 5.719782 at 70iterations 0.1352967 2.927624 at 80iterations 7.4282795E-02 1.850266 at 90iterations 4.0800456E-02 0.8469887 at 100iterations 2.2413556E-02 0.4925919 at 110iterations 1.2310640E-02 0.2559052 at 120iterations 6.7178039E-03 0.1437035 at 130iterations 3.6793875E-03 8.4941864E-02 at 140iterations 2.0173162E-03 4.2830944E-02 at 150iterations 1.1044125E-03 2.3130417E-02 at 160iterations 6.0372951E-04 1.3898849E-02 at 170iterations 3.2981433E-04 6.6437721E-03 at 180iterations finished qdiffx linear iterations at : 14:42:26 total time elapsed so far: 14.85000 # loops : 180 mean,max change (kT/e) : 3.2981433E-04 6.6437721E-03 energy calculations done at 14.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.04000 DelPhi exited at 14:42:27 15.041u 0.282s 0:15.60 98.2% 0+0k 0+0io 0pf+0w