Tue Oct 11 03:24:33 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 Tue Oct 11 2011 at 03:24:33 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5664010 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): -12.69200 38.83300 ymin,ymax (A): -1.756000 51.43300 zmin,zma (A): -17.24100 45.61200 x,y,z range (A): 51.52500 53.18900 62.85300 scale (grids/A): 0.5664010 object centre (A): 13.07050 24.83850 14.18550 number of atom coordinates read : 3067 total number of charged atoms : 2926 net assigned charge : 3.528027 assigned positive charge : 460.5628 centred at (gu) : 89.51535 90.25018 91.13145 assigned negative charge : -457.0362 centred at (gu) : 89.50764 90.30779 91.11590 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6529 nv = 96 ne = 84 npr = 60306 no. pairs analyzed = 60306 no. exposed pairs = 4439 no. arc points = 31477 no. surface atoms = 1464 nbur = 1603 mkacc time = 0.1300000 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= 305 mr = 3023 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3071 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9691608E-10 9.0996860E-10 midg,1,midg; midg,igrid,midg 1.2149960E-09 -3.7573181E-10 1,midg,midg; igrid,midg,midg 4.0742221E-10 5.2193627E-10 gauss-seidel spectral radius is 0.9839377 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 03:24:34 rms-change max change #iterations 9.1814838E-02 15.76102 at 10iterations 7.0484374E-03 1.039680 at 20iterations 7.4124045E-04 0.1281891 at 30iterations 1.5511531E-04 2.7638435E-02 at 40iterations 4.1719803E-05 7.7877045E-03 at 50iterations finished qdiffx linear iterations at : 03:24:37 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.1719803E-05 7.7877045E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 03:24:37 3.435u 0.219s 0:04.24 85.8% 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 Tue Oct 11 2011 at 03:24:37 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.699203 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): -12.69200 38.83300 ymin,ymax (A): -1.756000 51.43300 zmin,zma (A): -17.24100 45.61200 x,y,z range (A): 51.52500 53.18900 62.85300 scale (grids/A): 1.699203 object centre (A): 13.07050 24.83850 14.18550 number of atom coordinates read : 3067 total number of charged atoms : 2926 net assigned charge : 3.528027 assigned positive charge : 460.5628 centred at (gu) : 88.54476 90.74939 93.39359 assigned negative charge : -457.0362 centred at (gu) : 88.52252 90.92279 93.34724 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31477 grid for indexing accessible points = 1.400000 m= 22264 mr = 45128 m= 2686 mr = 14501 m= 106 mr = 1329 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 35099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 22584 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) : 0.5664010 object centre at (A) : 13.07050 24.83850 14.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3818577E-04 1.0143925E-02 midg,1,midg; midg,igrid,midg 1.0403906E-02 -7.4427803E-03 1,midg,midg; igrid,midg,midg 6.2028938E-03 1.7185267E-02 gauss-seidel spectral radius is 0.9983648 estimated iterations to convergence 196 setup time was (sec) 0.8200000 now iterating at: 03:24:38 rms-change max change #iterations 3.739584 145.1820 at 10iterations 1.615729 58.30709 at 20iterations 0.7013990 26.64051 at 30iterations 0.3039543 12.03553 at 40iterations 0.1326458 4.716724 at 50iterations 5.7674840E-02 2.218073 at 60iterations 2.5172837E-02 1.159653 at 70iterations 1.0986820E-02 0.4356270 at 80iterations 4.8202681E-03 0.1703796 at 90iterations 2.1331005E-03 7.5923920E-02 at 100iterations 9.5155538E-04 3.4507751E-02 at 110iterations 4.3965186E-04 1.5236855E-02 at 120iterations finished qdiffx linear iterations at : 03:24:46 total time elapsed so far: 8.380000 # loops : 120 mean,max change (kT/e) : 4.3965186E-04 1.5236855E-02 energy calculations done at 8.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.550000 DelPhi exited at 03:24:46 8.552u 0.220s 0:09.12 96.1% 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 Tue Oct 11 2011 at 03:24:47 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 has a net charge of 0.5140 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: 2.548805 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): -12.69200 38.83300 ymin,ymax (A): -1.756000 51.43300 zmin,zma (A): -17.24100 45.61200 x,y,z range (A): 51.52500 53.18900 62.85300 scale (grids/A): 2.548805 object centre (A): 13.07050 24.83850 14.18550 number of atom coordinates read : 3067 total number of charged atoms : 2926 net assigned charge : 3.528027 assigned positive charge : 460.5628 centred at (gu) : 87.81711 91.12386 95.09023 assigned negative charge : -457.0362 centred at (gu) : 87.78381 91.38403 95.02085 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 164511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31477 grid for indexing accessible points = 1.400000 m= 74712 mr = 111394 m= 23408 mr = 56777 m= 4384 mr = 17023 m= 395 mr = 2773 m= 7 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 79262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 23391 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) : 1.699203 object centre at (A) : 13.07050 24.83850 14.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9979197E-02 3.5449211E-02 midg,1,midg; midg,igrid,midg 0.1362975 -0.1639189 1,midg,midg; igrid,midg,midg 0.1182448 0.3531399 gauss-seidel spectral radius is 0.9992075 estimated iterations to convergence 280 setup time was (sec) 1.560000 now iterating at: 03:24:48 rms-change max change #iterations 9.538674 280.5599 at 10iterations 5.554868 144.1825 at 20iterations 3.199151 76.57251 at 30iterations 1.837438 42.98768 at 40iterations 1.049853 23.19366 at 50iterations 0.5981035 12.50960 at 60iterations 0.3394308 8.669488 at 70iterations 0.1922409 3.766647 at 80iterations 0.1091207 2.265125 at 90iterations 6.1667759E-02 1.288319 at 100iterations 3.4825929E-02 0.7135448 at 110iterations 1.9731294E-02 0.4147511 at 120iterations 1.1162576E-02 0.2232246 at 130iterations 6.3348352E-03 0.1300883 at 140iterations 3.6015976E-03 7.7045441E-02 at 150iterations 2.0612469E-03 4.2575836E-02 at 160iterations 1.2009082E-03 2.4072647E-02 at 170iterations 7.1047002E-04 1.4970779E-02 at 180iterations finished qdiffx linear iterations at : 03:24:59 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 7.1047002E-04 1.4970779E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 03:25:00 12.634u 0.244s 0:13.28 96.9% 0+0k 0+0io 0pf+0w