Sun Oct 9 08:54:21 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 08:54:21 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 = 5488 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: 0.5121565 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): 8.089999 77.60000 ymin,ymax (A): -30.57300 30.57900 zmin,zma (A): -17.86700 50.24300 x,y,z range (A): 69.51000 61.15200 68.11000 scale (grids/A): 0.5121565 object centre (A): 42.84500 3.0002594E-03 16.18800 number of atom coordinates read : 5488 total number of charged atoms : 5322 net assigned charge : -4.499980 assigned positive charge : 824.1790 centred at (gu) : 89.71159 90.39239 89.11336 assigned negative charge : -828.6857 centred at (gu) : 89.62738 90.48391 89.11391 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9170 nv = 96 ne = 84 npr = 110149 no. pairs analyzed = 110149 no. exposed pairs = 7058 no. arc points = 48447 no. surface atoms = 2361 nbur = 3127 mkacc time = 0.1900000 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 = 1.652000 m= 307 mr = 4697 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4756 ## 710 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12304 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0686069E-11 -5.4170429E-11 midg,1,midg; midg,igrid,midg 2.0202781E-10 -4.0388792E-10 1,midg,midg; igrid,midg,midg -3.6685857E-10 1.8648598E-10 gauss-seidel spectral radius is 0.9805555 estimated iterations to convergence 59 setup time was (sec) 0.5400000 now iterating at: 08:54:22 rms-change max change #iterations 7.4573845E-02 10.04392 at 10iterations 4.4983840E-03 0.6959381 at 20iterations 5.4299168E-04 0.1176052 at 30iterations 1.5993934E-04 3.4936905E-02 at 40iterations 5.3311571E-05 1.1354446E-02 at 50iterations finished qdiffx linear iterations at : 08:54:24 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 5.3311571E-05 1.1354446E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 08:54:25 3.540u 0.176s 0:04.00 92.7% 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 08:54:25 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 = 5488 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: 1.536470 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): 8.089999 77.60000 ymin,ymax (A): -30.57300 30.57900 zmin,zma (A): -17.86700 50.24300 x,y,z range (A): 69.51000 61.15200 68.11000 scale (grids/A): 1.536470 object centre (A): 42.84500 3.0002594E-03 16.18800 number of atom coordinates read : 5488 total number of charged atoms : 5322 net assigned charge : -4.499980 assigned positive charge : 824.1790 centred at (gu) : 89.13282 91.17531 87.33887 assigned negative charge : -828.6857 centred at (gu) : 88.88180 91.45142 87.34157 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 103913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48447 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30313 mr = 71342 m= 2447 mr = 19780 m= 48 mr = 915 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 911 time to turn everything in is 0.4900000 number of dielectric boundary points 44684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 679 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 40036 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) : 0.5121565 object centre at (A) : 42.84500 3.0002594E-03 16.18800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6125340E-02 -1.8481592E-02 midg,1,midg; midg,igrid,midg 6.3986075E-03 -6.0258717E-03 1,midg,midg; igrid,midg,midg -2.1762749E-02 7.5539725E-04 gauss-seidel spectral radius is 0.9981970 estimated iterations to convergence 187 setup time was (sec) 0.7200000 now iterating at: 08:54:26 rms-change max change #iterations 4.137918 174.4957 at 10iterations 1.734121 60.72499 at 20iterations 0.7231228 23.88329 at 30iterations 0.3038599 8.770840 at 40iterations 0.1272374 3.884705 at 50iterations 5.3459201E-02 1.929377 at 60iterations 2.2420188E-02 0.6472492 at 70iterations 9.4343005E-03 0.3354597 at 80iterations 3.9885431E-03 0.1175213 at 90iterations 1.7147871E-03 5.9638977E-02 at 100iterations 7.5699179E-04 2.7002335E-02 at 110iterations 3.5452537E-04 1.2794495E-02 at 120iterations finished qdiffx linear iterations at : 08:54:33 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 3.5452537E-04 1.2794495E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 08:54:33 7.990u 0.200s 0:08.45 96.9% 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 08:54:33 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 = 5488 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: 2.304704 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): 8.089999 77.60000 ymin,ymax (A): -30.57300 30.57900 zmin,zma (A): -17.86700 50.24300 x,y,z range (A): 69.51000 61.15200 68.11000 scale (grids/A): 2.304704 object centre (A): 42.84500 3.0002594E-03 16.18800 number of atom coordinates read : 5488 total number of charged atoms : 5322 net assigned charge : -4.499980 assigned positive charge : 824.1790 centred at (gu) : 88.69884 91.76269 86.00777 assigned negative charge : -828.6857 centred at (gu) : 88.32265 92.17693 86.01226 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 241920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48447 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 108827 mr = 175467 m= 26789 mr = 84077 m= 3368 mr = 18695 m= 166 mr = 1915 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 3041 time to turn everything in is 1.210000 number of dielectric boundary points 100866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 42440 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) : 1.536470 object centre at (A) : 42.84500 3.0002594E-03 16.18800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3344535 -0.4371499 midg,1,midg; midg,igrid,midg 9.8970480E-02 -9.4507679E-02 1,midg,midg; igrid,midg,midg -0.6401820 4.7090895E-02 gauss-seidel spectral radius is 0.9992128 estimated iterations to convergence 281 setup time was (sec) 1.460000 now iterating at: 08:54:35 rms-change max change #iterations 11.30309 303.6516 at 10iterations 6.659451 171.0807 at 20iterations 3.877236 83.32872 at 30iterations 2.243798 48.78239 at 40iterations 1.295537 24.14935 at 50iterations 0.7435902 14.03747 at 60iterations 0.4261228 9.075665 at 70iterations 0.2442112 4.300777 at 80iterations 0.1393295 2.982197 at 90iterations 7.9454377E-02 1.464924 at 100iterations 4.5183897E-02 0.8468771 at 110iterations 2.5775623E-02 0.4467392 at 120iterations 1.4649457E-02 0.2805138 at 130iterations 8.3281407E-03 0.1472130 at 140iterations 4.7480571E-03 9.8646164E-02 at 150iterations 2.7007475E-03 5.0876617E-02 at 160iterations 1.5508983E-03 2.7938843E-02 at 170iterations 8.8984257E-04 1.6048431E-02 at 180iterations finished qdiffx linear iterations at : 08:54:47 total time elapsed so far: 13.30000 # loops : 180 mean,max change (kT/e) : 8.8984257E-04 1.6048431E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 08:54:47 13.432u 0.218s 0:13.92 97.9% 0+0k 0+0io 0pf+0w