Mon Oct 10 19:37:02 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 Mon Oct 10 2011 at 19:37:02 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 = 2873 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5726419 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): -16.97200 32.25900 ymin,ymax (A): 8.087999 57.74000 zmin,zma (A): 12.76400 74.93200 x,y,z range (A): 49.23100 49.65200 62.16800 scale (grids/A): 0.5726419 object centre (A): 7.643499 32.91400 43.84800 number of atom coordinates read : 2873 total number of charged atoms : 2732 net assigned charge : 2.000025 assigned positive charge : 427.0125 centred at (gu) : 90.25268 90.70964 90.11145 assigned negative charge : -425.0135 centred at (gu) : 90.28878 90.57552 90.23814 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6021 nv = 96 ne = 84 npr = 58319 no. pairs analyzed = 58319 no. exposed pairs = 3865 no. arc points = 27158 no. surface atoms = 1306 nbur = 1567 mkacc time = 0.1600000 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= 302 mr = 2961 m= 4 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2704 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 7875 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3167264E-09 -1.8382359E-09 midg,1,midg; midg,igrid,midg -1.6122053E-09 2.9625780E-09 1,midg,midg; igrid,midg,midg 8.6499757E-10 -2.8736974E-10 gauss-seidel spectral radius is 0.9842565 estimated iterations to convergence 65 setup time was (sec) 0.7200000 now iterating at: 19:37:03 rms-change max change #iterations 9.1152400E-02 16.74057 at 10iterations 6.7748381E-03 1.302956 at 20iterations 5.1097258E-04 8.0062866E-02 at 30iterations 4.0663595E-05 6.5064430E-03 at 40iterations 3.9820270E-06 6.9046021E-04 at 50iterations finished qdiffx linear iterations at : 19:37:06 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 3.9820270E-06 6.9046021E-04 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 19:37:07 4.332u 0.210s 0:05.03 90.2% 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 19:37:07 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 = 2873 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.717926 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): -16.97200 32.25900 ymin,ymax (A): 8.087999 57.74000 zmin,zma (A): 12.76400 74.93200 x,y,z range (A): 49.23100 49.65200 62.16800 scale (grids/A): 1.717926 object centre (A): 7.643499 32.91400 43.84800 number of atom coordinates read : 2873 total number of charged atoms : 2732 net assigned charge : 2.000025 assigned positive charge : 427.0125 centred at (gu) : 90.75745 92.12849 90.33367 assigned negative charge : -425.0135 centred at (gu) : 90.86629 91.72625 90.71390 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 65115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27158 grid for indexing accessible points = 1.400000 m= 21137 mr = 42337 m= 2968 mr = 14470 m= 114 mr = 1638 m= 0 mr = 13 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 30876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21168 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) : 0.5726419 object centre at (A) : 7.643499 32.91400 43.84800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5866074E-03 -9.5899049E-03 midg,1,midg; midg,igrid,midg -1.5084302E-02 1.2755030E-02 1,midg,midg; igrid,midg,midg -4.2384760E-03 6.9984881E-04 gauss-seidel spectral radius is 0.9983613 estimated iterations to convergence 196 setup time was (sec) 1.010000 now iterating at: 19:37:08 rms-change max change #iterations 3.615395 184.3265 at 10iterations 1.563725 61.96652 at 20iterations 0.6817703 24.09887 at 30iterations 0.2973434 10.41109 at 40iterations 0.1286318 4.438602 at 50iterations 5.6294776E-02 1.890276 at 60iterations 2.4488937E-02 0.8632445 at 70iterations 1.0649679E-02 0.4029932 at 80iterations 4.6342975E-03 0.1580181 at 90iterations 2.0294031E-03 6.5974236E-02 at 100iterations 8.8309636E-04 2.9922485E-02 at 110iterations 3.8474903E-04 1.3818741E-02 at 120iterations finished qdiffx linear iterations at : 19:37:16 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 3.8474903E-04 1.3818741E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 19:37:17 9.588u 0.241s 0:10.28 95.5% 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 19:37:17 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 = 2873 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.576889 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): -16.97200 32.25900 ymin,ymax (A): 8.087999 57.74000 zmin,zma (A): 12.76400 74.93200 x,y,z range (A): 49.23100 49.65200 62.16800 scale (grids/A): 2.576889 object centre (A): 7.643499 32.91400 43.84800 number of atom coordinates read : 2873 total number of charged atoms : 2732 net assigned charge : 2.000025 assigned positive charge : 427.0125 centred at (gu) : 91.13607 93.19255 90.50031 assigned negative charge : -425.0135 centred at (gu) : 91.29925 92.58938 91.07085 start vw surface at 0.2000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 150638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27158 grid for indexing accessible points = 1.400000 m= 69932 mr = 103705 m= 23460 mr = 54489 m= 5055 mr = 17899 m= 437 mr = 3585 m= 3 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 69651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 21842 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) : 1.717926 object centre at (A) : 7.643499 32.91400 43.84800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2069450E-02 -4.6922810E-02 midg,1,midg; midg,igrid,midg -0.1974753 0.1582947 1,midg,midg; igrid,midg,midg -0.1106164 -3.2137975E-02 gauss-seidel spectral radius is 0.9991954 estimated iterations to convergence 278 setup time was (sec) 1.950000 now iterating at: 19:37:19 rms-change max change #iterations 9.084186 351.4392 at 10iterations 5.192080 133.0301 at 20iterations 2.963753 70.29935 at 30iterations 1.678058 38.45472 at 40iterations 0.9468591 22.03171 at 50iterations 0.5347441 13.77901 at 60iterations 0.3003312 6.723524 at 70iterations 0.1692632 3.425024 at 80iterations 9.4984017E-02 1.954731 at 90iterations 5.3420283E-02 1.102318 at 100iterations 2.9966846E-02 0.5879565 at 110iterations 1.6798809E-02 0.3318253 at 120iterations 9.4381720E-03 0.1995821 at 130iterations 5.2788192E-03 0.1056242 at 140iterations 2.9615106E-03 5.8698654E-02 at 150iterations 1.6598464E-03 3.2939911E-02 at 160iterations 9.3186286E-04 1.8211842E-02 at 170iterations 5.2170979E-04 1.0567665E-02 at 180iterations finished qdiffx linear iterations at : 19:37:33 total time elapsed so far: 15.16000 # loops : 180 mean,max change (kT/e) : 5.2170979E-04 1.0567665E-02 energy calculations done at 15.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.39000 DelPhi exited at 19:37:34 15.392u 0.272s 0:16.57 94.5% 0+0k 0+0io 0pf+0w