Sat Oct 15 12:48:23 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+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 Sat Oct 15 2011 at 12:48:23 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5920703 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): -79.77600 -32.39600 ymin,ymax (A): -32.86000 27.26800 zmin,zma (A): -52.05600 5.891000 x,y,z range (A): 47.38000 60.12800 57.94700 scale (grids/A): 0.5920703 object centre (A): -56.08600 -2.796000 -23.08250 number of atom coordinates read : 2688 total number of charged atoms : 2543 net assigned charge : -1.999981 assigned positive charge : 399.6627 centred at (gu) : 89.58295 88.51791 88.51843 assigned negative charge : -401.6634 centred at (gu) : 89.50685 88.71232 88.57947 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6421 nv = 96 ne = 84 npr = 53205 no. pairs analyzed = 53205 no. exposed pairs = 3712 no. arc points = 26257 no. surface atoms = 1221 nbur = 1467 mkacc time = 9.0000004E-02 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 = 1.456000 m= 345 mr = 3263 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2000000 number of dielectric boundary points 3472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2579 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7922 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4546013E-09 -1.8270844E-09 midg,1,midg; midg,igrid,midg 6.8379076E-09 -4.6822244E-09 1,midg,midg; igrid,midg,midg -3.3204566E-09 1.3112311E-09 gauss-seidel spectral radius is 0.9852572 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 12:48:24 rms-change max change #iterations 0.1052017 18.06474 at 10iterations 8.6294021E-03 1.436986 at 20iterations 7.5568684E-04 0.1208420 at 30iterations 1.0377784E-04 2.2626877E-02 at 40iterations 2.5819789E-05 6.5803528E-03 at 50iterations finished qdiffx linear iterations at : 12:48:28 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 2.5819789E-05 6.5803528E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 12:48:29 3.991u 0.263s 0:05.56 76.4% 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 Sat Oct 15 2011 at 12:48:29 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.776211 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): -79.77600 -32.39600 ymin,ymax (A): -32.86000 27.26800 zmin,zma (A): -52.05600 5.891000 x,y,z range (A): 47.38000 60.12800 57.94700 scale (grids/A): 1.776211 object centre (A): -56.08600 -2.796000 -23.08250 number of atom coordinates read : 2688 total number of charged atoms : 2543 net assigned charge : -1.999981 assigned positive charge : 399.6627 centred at (gu) : 88.74831 85.55313 85.55456 assigned negative charge : -401.6634 centred at (gu) : 88.52038 86.13676 85.73815 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69222 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26257 grid for indexing accessible points = 1.400000 m= 23716 mr = 45710 m= 3311 mr = 16743 m= 153 mr = 1897 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.3700000 number of dielectric boundary points 32013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19822 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) : 0.5920703 object centre at (A) : -56.08600 -2.796000 -23.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4100121E-02 -1.7280437E-02 midg,1,midg; midg,igrid,midg 3.4691745E-03 -2.9189233E-02 1,midg,midg; igrid,midg,midg 7.5178579E-03 9.9971788E-03 gauss-seidel spectral radius is 0.9984542 estimated iterations to convergence 202 setup time was (sec) 0.6100000 now iterating at: 12:48:30 rms-change max change #iterations 3.779505 170.4634 at 10iterations 1.673724 62.91231 at 20iterations 0.7433099 24.19835 at 30iterations 0.3299295 10.27704 at 40iterations 0.1468382 4.685906 at 50iterations 6.5473810E-02 2.230927 at 60iterations 2.9103281E-02 1.138358 at 70iterations 1.2958952E-02 0.4416981 at 80iterations 5.7893610E-03 0.1950321 at 90iterations 2.5939995E-03 9.0316772E-02 at 100iterations 1.1589050E-03 4.0547848E-02 at 110iterations 5.2106206E-04 1.8215179E-02 at 120iterations finished qdiffx linear iterations at : 12:48:40 total time elapsed so far: 8.970000 # loops : 120 mean,max change (kT/e) : 5.2106206E-04 1.8215179E-02 energy calculations done at 8.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.110000 DelPhi exited at 12:48:41 9.114u 0.282s 0:11.80 79.5% 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 Sat Oct 15 2011 at 12:48:41 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.664316 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): -79.77600 -32.39600 ymin,ymax (A): -32.86000 27.26800 zmin,zma (A): -52.05600 5.891000 x,y,z range (A): 47.38000 60.12800 57.94700 scale (grids/A): 2.664316 object centre (A): -56.08600 -2.796000 -23.08250 number of atom coordinates read : 2688 total number of charged atoms : 2543 net assigned charge : -1.999981 assigned positive charge : 399.6627 centred at (gu) : 88.12253 83.32944 83.33175 assigned negative charge : -401.6634 centred at (gu) : 87.78059 84.20504 83.60721 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 160159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26257 grid for indexing accessible points = 1.400000 m= 77427 mr = 111643 m= 26655 mr = 61613 m= 5641 mr = 20580 m= 669 mr = 4030 m= 18 mr = 424 m= 0 mr = 3 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 581 time to turn everything in is 0.9200000 number of dielectric boundary points 72276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 20338 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) : 1.776211 object centre at (A) : -56.08600 -2.796000 -23.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1159705 -0.1973608 midg,1,midg; midg,igrid,midg -6.7153655E-02 -0.3342452 1,midg,midg; igrid,midg,midg 0.1219284 0.1402168 gauss-seidel spectral radius is 0.9992165 estimated iterations to convergence 282 setup time was (sec) 1.210000 now iterating at: 12:48:43 rms-change max change #iterations 9.399660 286.8200 at 10iterations 5.466830 151.4883 at 20iterations 3.158957 89.91118 at 30iterations 1.807154 40.96891 at 40iterations 1.032835 20.48622 at 50iterations 0.5873529 11.65585 at 60iterations 0.3343135 6.687263 at 70iterations 0.1897414 4.310686 at 80iterations 0.1075582 2.335052 at 90iterations 6.0942922E-02 1.378210 at 100iterations 3.4548510E-02 0.7877846 at 110iterations 1.9570289E-02 0.3418178 at 120iterations 1.1070641E-02 0.2131500 at 130iterations 6.2749833E-03 0.1290359 at 140iterations 3.5615820E-03 6.5994263E-02 at 150iterations 2.0342085E-03 3.8852692E-02 at 160iterations 1.1690006E-03 2.3480177E-02 at 170iterations 6.8038085E-04 1.5426636E-02 at 180iterations finished qdiffx linear iterations at : 12:48:59 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 6.8038085E-04 1.5426636E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.23000 DelPhi exited at 12:48:59 15.229u 0.322s 0:18.50 84.0% 0+0k 0+0io 0pf+0w