Mon Oct 10 18:52:27 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 18:52:27 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 = 4112 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: 0.5529324 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): -75.47600 -16.08100 ymin,ymax (A): -40.30300 24.08100 zmin,zma (A): 198.2420 257.7090 x,y,z range (A): 59.39500 64.38400 59.46703 scale (grids/A): 0.5529324 object centre (A): -45.77850 -8.110998 227.9755 number of atom coordinates read : 4112 total number of charged atoms : 3963 net assigned charge : 2.500035 assigned positive charge : 631.1567 centred at (gu) : 90.13476 91.97664 87.73540 assigned negative charge : -628.6601 centred at (gu) : 90.21120 91.90803 87.83482 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 81633 no. pairs analyzed = 81633 no. exposed pairs = 5382 no. arc points = 37361 no. surface atoms = 1797 nbur = 2315 mkacc time = 0.2100000 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 = 1.540000 m= 348 mr = 4290 m= 0 mr = 11 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.4400000 number of dielectric boundary points 4266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3775 ## 499 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3549616E-09 -6.0157157E-10 midg,1,midg; midg,igrid,midg -4.1316164E-10 1.5928162E-09 1,midg,midg; igrid,midg,midg 1.0305110E-09 -7.9908058E-10 gauss-seidel spectral radius is 0.9832222 estimated iterations to convergence 64 setup time was (sec) 0.7400000 now iterating at: 18:52:28 rms-change max change #iterations 8.9770392E-02 16.50533 at 10iterations 6.7871981E-03 0.9265118 at 20iterations 1.0691076E-03 0.2531166 at 30iterations 4.2637502E-04 0.1060257 at 40iterations 2.0281311E-04 4.7042847E-02 at 50iterations finished qdiffx linear iterations at : 18:52:32 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 2.0281311E-04 4.7042847E-02 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 18:52:33 4.677u 0.411s 0:05.52 92.0% 0+0k 0+0io 6pf+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 18:52:33 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 = 4112 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: 1.658797 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): -75.47600 -16.08100 ymin,ymax (A): -40.30300 24.08100 zmin,zma (A): 198.2420 257.7090 x,y,z range (A): 59.39500 64.38400 59.46703 scale (grids/A): 1.658797 object centre (A): -45.77850 -8.110998 227.9755 number of atom coordinates read : 4112 total number of charged atoms : 3963 net assigned charge : 2.500035 assigned positive charge : 631.1567 centred at (gu) : 90.40301 95.92847 83.20474 assigned negative charge : -628.6601 centred at (gu) : 90.63318 95.72387 83.50420 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 90571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37361 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29782 mr = 61917 m= 3409 mr = 20713 m= 105 mr = 1765 m= 0 mr = 5 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 632 time to turn everything in is 0.7600000 number of dielectric boundary points 39467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 425 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 30404 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) : 0.5529324 object centre at (A) : -45.77850 -8.110998 227.9755 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4002919E-03 -1.2913084E-02 midg,1,midg; midg,igrid,midg -1.2039268E-02 2.0689774E-02 1,midg,midg; igrid,midg,midg 1.2465474E-03 3.7122744E-03 gauss-seidel spectral radius is 0.9983544 estimated iterations to convergence 196 setup time was (sec) 1.070000 now iterating at: 18:52:34 rms-change max change #iterations 4.173200 150.2482 at 10iterations 1.813857 59.88564 at 20iterations 0.7907607 25.67198 at 30iterations 0.3441067 10.93744 at 40iterations 0.1501454 4.787937 at 50iterations 6.5391943E-02 2.108153 at 60iterations 2.8595630E-02 0.8734360 at 70iterations 1.2522591E-02 0.3858948 at 80iterations 5.5618528E-03 0.1824875 at 90iterations 2.5607045E-03 9.3070984E-02 at 100iterations 1.2692374E-03 5.3268433E-02 at 110iterations 7.2966865E-04 2.8320313E-02 at 120iterations finished qdiffx linear iterations at : 18:52:44 total time elapsed so far: 10.73000 # loops : 120 mean,max change (kT/e) : 7.2966865E-04 2.8320313E-02 energy calculations done at 10.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.88000 DelPhi exited at 18:52:44 10.883u 0.461s 0:11.67 97.1% 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 Mon Oct 10 2011 at 18:52:44 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 = 4112 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: 2.488196 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): -75.47600 -16.08100 ymin,ymax (A): -40.30300 24.08100 zmin,zma (A): 198.2420 257.7090 x,y,z range (A): 59.39500 64.38400 59.46703 scale (grids/A): 2.488196 object centre (A): -45.77850 -8.110998 227.9755 number of atom coordinates read : 4112 total number of charged atoms : 3963 net assigned charge : 2.500035 assigned positive charge : 631.1567 centred at (gu) : 90.60423 98.89239 79.80687 assigned negative charge : -628.6601 centred at (gu) : 90.94968 98.58569 80.25619 start vw surface at 0.1600000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 210487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37361 grid for indexing accessible points = 1.400000 m= 100655 mr = 151785 m= 30634 mr = 79730 m= 5469 mr = 23174 m= 481 mr = 3669 m= 9 mr = 238 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 2038 time to turn everything in is 1.870000 number of dielectric boundary points 89139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 31679 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) : 1.658797 object centre at (A) : -45.77850 -8.110998 227.9755 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8629004E-02 -0.1795644 midg,1,midg; midg,igrid,midg -0.5335230 0.3876731 1,midg,midg; igrid,midg,midg -5.9619825E-02 5.7861693E-02 gauss-seidel spectral radius is 0.9992173 estimated iterations to convergence 282 setup time was (sec) 2.210000 now iterating at: 18:52:47 rms-change max change #iterations 10.82138 362.4128 at 10iterations 6.298522 131.8551 at 20iterations 3.655341 76.31030 at 30iterations 2.104005 44.93934 at 40iterations 1.210524 24.67250 at 50iterations 0.6921084 12.72476 at 60iterations 0.3950885 7.979162 at 70iterations 0.2250859 4.072851 at 80iterations 0.1282040 2.476912 at 90iterations 7.2802827E-02 1.251074 at 100iterations 4.1421395E-02 0.8267174 at 110iterations 2.3582911E-02 0.4113731 at 120iterations 1.3417399E-02 0.2321930 at 130iterations 7.6464401E-03 0.1467934 at 140iterations 4.3659620E-03 8.2477570E-02 at 150iterations 2.5121504E-03 4.9140930E-02 at 160iterations 1.4854227E-03 3.4896851E-02 at 170iterations 9.0352574E-04 2.0530701E-02 at 180iterations finished qdiffx linear iterations at : 18:53:04 total time elapsed so far: 19.13000 # loops : 180 mean,max change (kT/e) : 9.0352574E-04 2.0530701E-02 energy calculations done at 19.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.29000 DelPhi exited at 18:53:05 19.299u 0.480s 0:20.32 97.2% 0+0k 0+0io 0pf+0w