Thu Jan 19 11:43:22 PST 2012 #!/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 Thu Jan 19 2012 at 11:43:22 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4918418 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): -35.93500 25.64700 ymin,ymax (A): -12.42000 55.71900 zmin,zma (A): 2.376000 74.75700 x,y,z range (A): 61.58200 68.13900 72.38100 scale (grids/A): 0.4918418 object centre (A): -5.144001 21.64950 38.56650 number of atom coordinates read : 5133 total number of charged atoms : 4960 net assigned charge : 23.99995 assigned positive charge : 790.0186 centred at (gu) : 90.50157 91.34646 90.82153 assigned negative charge : -766.0244 centred at (gu) : 90.43182 91.36246 90.84524 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 100446 no. pairs analyzed = 100446 no. exposed pairs = 6437 no. arc points = 44374 no. surface atoms = 2163 nbur = 2970 mkacc time = 0.2600000 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 = 1.736000 m= 255 mr = 4034 m= 0 mr = 4 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4308 ## 706 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 10619 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3752718E-10 1.4144308E-10 midg,1,midg; midg,igrid,midg 1.1335815E-10 1.7620677E-10 1,midg,midg; igrid,midg,midg 5.0900714E-11 2.5877084E-10 gauss-seidel spectral radius is 0.9788961 estimated iterations to convergence 57 setup time was (sec) 0.8600000 now iterating at: 11:43:24 rms-change max change #iterations 5.8416825E-02 10.31524 at 10iterations 4.1747787E-03 0.5601196 at 20iterations 1.1942097E-03 9.8863602E-02 at 30iterations 4.7549425E-04 3.9105415E-02 at 40iterations 1.9191419E-04 1.5889168E-02 at 50iterations finished qdiffx linear iterations at : 11:43:28 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 1.9191419E-04 1.5889168E-02 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.360000 DelPhi exited at 11:43:28 5.360u 0.436s 0:06.34 91.3% 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 Thu Jan 19 2012 at 11:43:29 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.475525 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): -35.93500 25.64700 ymin,ymax (A): -12.42000 55.71900 zmin,zma (A): 2.376000 74.75700 x,y,z range (A): 61.58200 68.13900 72.38100 scale (grids/A): 1.475525 object centre (A): -5.144001 21.64950 38.56650 number of atom coordinates read : 5133 total number of charged atoms : 4960 net assigned charge : 23.99995 assigned positive charge : 790.0186 centred at (gu) : 91.50355 94.03770 92.46301 assigned negative charge : -766.0244 centred at (gu) : 91.29531 94.08717 92.53571 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 90899 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 24714 mr = 62558 m= 1583 mr = 15944 m= 22 mr = 464 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2427 time to turn everything in is 0.7600000 number of dielectric boundary points 38252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 697 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 36764 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) : 0.4918418 object centre at (A) : -5.144001 21.64950 38.56650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6583402E-03 6.5119407E-04 midg,1,midg; midg,igrid,midg -5.1984342E-04 6.1758631E-03 1,midg,midg; igrid,midg,midg 8.4487144E-03 2.1417253E-02 gauss-seidel spectral radius is 0.9979845 estimated iterations to convergence 177 setup time was (sec) 1.150000 now iterating at: 11:43:30 rms-change max change #iterations 3.673700 171.3298 at 10iterations 1.462357 49.60962 at 20iterations 0.5846482 19.40512 at 30iterations 0.2339258 7.867859 at 40iterations 9.3549810E-02 3.261383 at 50iterations 3.7577033E-02 1.238489 at 60iterations 1.5224875E-02 0.4593964 at 70iterations 6.3647926E-03 0.2062912 at 80iterations 2.8313098E-03 9.2624664E-02 at 90iterations 1.4387516E-03 4.0336609E-02 at 100iterations 8.5191755E-04 2.3887634E-02 at 110iterations 5.6183414E-04 1.2093544E-02 at 120iterations finished qdiffx linear iterations at : 11:43:41 total time elapsed so far: 12.17000 # loops : 120 mean,max change (kT/e) : 5.6183414E-04 1.2093544E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 11:43:42 12.343u 0.497s 0:13.30 96.4% 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 Thu Jan 19 2012 at 11:43:42 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.213288 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): -35.93500 25.64700 ymin,ymax (A): -12.42000 55.71900 zmin,zma (A): 2.376000 74.75700 x,y,z range (A): 61.58200 68.13900 72.38100 scale (grids/A): 2.213288 object centre (A): -5.144001 21.64950 38.56650 number of atom coordinates read : 5133 total number of charged atoms : 4960 net assigned charge : 23.99995 assigned positive charge : 790.0186 centred at (gu) : 92.25481 96.05626 93.69407 assigned negative charge : -766.0244 centred at (gu) : 91.94312 96.13066 93.80346 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 212293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 92305 mr = 154119 m= 19506 mr = 71569 m= 1892 mr = 13258 m= 59 mr = 904 m= 0 mr = 5 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 8346 time to turn everything in is 1.830000 number of dielectric boundary points 86200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 39533 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) : 1.475525 object centre at (A) : -5.144001 21.64950 38.56650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2021352 3.7558790E-02 midg,1,midg; midg,igrid,midg -5.0926268E-02 -0.1002628 1,midg,midg; igrid,midg,midg 0.1299149 0.3503090 gauss-seidel spectral radius is 0.9991416 estimated iterations to convergence 270 setup time was (sec) 2.230000 now iterating at: 11:43:45 rms-change max change #iterations 10.24192 310.6537 at 10iterations 5.844029 174.8150 at 20iterations 3.317349 82.88840 at 30iterations 1.876120 41.40375 at 40iterations 1.058110 23.69543 at 50iterations 0.5938088 12.99462 at 60iterations 0.3331539 7.494759 at 70iterations 0.1865485 3.740685 at 80iterations 0.1041931 2.372379 at 90iterations 5.8027275E-02 1.129908 at 100iterations 3.2292437E-02 0.6198273 at 110iterations 1.7976897E-02 0.3788681 at 120iterations 9.9874642E-03 0.2022095 at 130iterations 5.5580051E-03 0.1160393 at 140iterations 3.0956981E-03 6.0037613E-02 at 150iterations 1.7238581E-03 3.4473419E-02 at 160iterations 9.6232648E-04 2.0931959E-02 at 170iterations 5.4219092E-04 1.1665344E-02 at 180iterations finished qdiffx linear iterations at : 11:44:04 total time elapsed so far: 21.34000 # loops : 180 mean,max change (kT/e) : 5.4219092E-04 1.1665344E-02 energy calculations done at 21.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.50000 DelPhi exited at 11:44:04 21.509u 0.547s 0:22.35 98.6% 0+0k 0+0io 0pf+0w