Sat Oct 15 15:02:13 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 15:02:13 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5695726 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): 18.07700 80.58000 ymin,ymax (A): -11.49700 44.02000 zmin,zma (A): -7.938000 35.14100 x,y,z range (A): 62.50300 55.51700 43.07900 scale (grids/A): 0.5695726 object centre (A): 49.32850 16.26150 13.60150 number of atom coordinates read : 2629 total number of charged atoms : 2479 net assigned charge : 5.812024 assigned positive charge : 394.6788 centred at (gu) : 87.43530 89.76896 89.69869 assigned negative charge : -388.8675 centred at (gu) : 87.67329 89.90694 89.84805 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5547 nv = 96 ne = 84 npr = 53283 no. pairs analyzed = 53283 no. exposed pairs = 3077 no. arc points = 22006 no. surface atoms = 1041 nbur = 1588 mkacc time = 0.1500000 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= 221 mr = 3024 m= 0 mr = 15 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3500000 number of dielectric boundary points 2729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7138 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9536487E-09 -1.1800184E-09 midg,1,midg; midg,igrid,midg 2.7481479E-09 -1.0511102E-09 1,midg,midg; igrid,midg,midg 7.2542727E-09 -1.3523459E-09 gauss-seidel spectral radius is 0.9840626 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 15:02:14 rms-change max change #iterations 8.7656304E-02 17.03601 at 10iterations 7.3876055E-03 1.548958 at 20iterations 9.4950909E-04 0.2398491 at 30iterations 2.0621008E-04 5.6190491E-02 at 40iterations 4.7759142E-05 1.3267517E-02 at 50iterations finished qdiffx linear iterations at : 15:02:17 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 4.7759142E-05 1.3267517E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 15:02:18 4.171u 0.285s 0:04.75 93.6% 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 15:02:18 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.708718 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): 18.07700 80.58000 ymin,ymax (A): -11.49700 44.02000 zmin,zma (A): -7.938000 35.14100 x,y,z range (A): 62.50300 55.51700 43.07900 scale (grids/A): 1.708718 object centre (A): 49.32850 16.26150 13.60150 number of atom coordinates read : 2629 total number of charged atoms : 2479 net assigned charge : 5.812024 assigned positive charge : 394.6788 centred at (gu) : 82.30547 89.30602 89.09556 assigned negative charge : -388.8675 centred at (gu) : 83.01958 89.72045 89.54391 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 61582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22006 grid for indexing accessible points = 1.400000 m= 19342 mr = 42972 m= 2213 mr = 13784 m= 65 mr = 1208 m= 0 mr = 9 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2301 time to turn everything in is 0.5500000 number of dielectric boundary points 25229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19200 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) : 0.5695726 object centre at (A) : 49.32850 16.26150 13.60150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5770949E-02 9.2274253E-04 midg,1,midg; midg,igrid,midg 1.8390194E-02 -2.0091377E-02 1,midg,midg; igrid,midg,midg 7.3993211E-03 2.6286894E-03 gauss-seidel spectral radius is 0.9983023 estimated iterations to convergence 193 setup time was (sec) 0.8600000 now iterating at: 15:02:19 rms-change max change #iterations 3.390752 156.5793 at 10iterations 1.448512 52.81781 at 20iterations 0.6231779 22.69865 at 30iterations 0.2663642 10.38523 at 40iterations 0.1149866 4.689117 at 50iterations 4.9777973E-02 1.767963 at 60iterations 2.1477537E-02 0.7185116 at 70iterations 9.3566058E-03 0.3539581 at 80iterations 4.1224025E-03 0.1662331 at 90iterations 1.8892424E-03 8.2939148E-02 at 100iterations 9.1241562E-04 3.9142609E-02 at 110iterations 4.6287948E-04 2.1717072E-02 at 120iterations finished qdiffx linear iterations at : 15:02:27 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 4.6287948E-04 2.1717072E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 15:02:28 9.417u 0.318s 0:10.12 96.0% 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 15:02:28 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.563077 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): 18.07700 80.58000 ymin,ymax (A): -11.49700 44.02000 zmin,zma (A): -7.938000 35.14100 x,y,z range (A): 62.50300 55.51700 43.07900 scale (grids/A): 2.563077 object centre (A): 49.32850 16.26150 13.60150 number of atom coordinates read : 2629 total number of charged atoms : 2479 net assigned charge : 5.812024 assigned positive charge : 394.6788 centred at (gu) : 78.45811 88.95900 88.64320 assigned negative charge : -388.8675 centred at (gu) : 79.52939 89.58068 89.31593 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 143134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22006 grid for indexing accessible points = 1.400000 m= 66994 mr = 104570 m= 19841 mr = 54253 m= 3565 mr = 15397 m= 258 mr = 2505 m= 3 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 7733 time to turn everything in is 1.340000 number of dielectric boundary points 56949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 19820 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) : 1.708718 object centre at (A) : 49.32850 16.26150 13.60150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1792113 1.9644327E-02 midg,1,midg; midg,igrid,midg 0.2308600 -0.4379154 1,midg,midg; igrid,midg,midg -4.7981772E-03 0.1754004 gauss-seidel spectral radius is 0.9991592 estimated iterations to convergence 272 setup time was (sec) 1.660000 now iterating at: 15:02:30 rms-change max change #iterations 8.384593 264.5689 at 10iterations 4.643348 112.7572 at 20iterations 2.586607 60.12131 at 30iterations 1.432497 32.18502 at 40iterations 0.7944453 17.54731 at 50iterations 0.4409209 9.437653 at 60iterations 0.2437191 5.159782 at 70iterations 0.1349680 2.685360 at 80iterations 7.4805647E-02 1.584675 at 90iterations 4.1467994E-02 0.8514190 at 100iterations 2.2997532E-02 0.5476761 at 110iterations 1.2835822E-02 0.2781353 at 120iterations 7.2209365E-03 0.1480560 at 130iterations 4.1041700E-03 9.1247559E-02 at 140iterations 2.3726530E-03 5.9574127E-02 at 150iterations 1.4249011E-03 3.8730621E-02 at 160iterations 8.8759052E-04 2.4524689E-02 at 170iterations 5.7921343E-04 1.6246796E-02 at 180iterations finished qdiffx linear iterations at : 15:02:44 total time elapsed so far: 15.22000 # loops : 180 mean,max change (kT/e) : 5.7921343E-04 1.6246796E-02 energy calculations done at 15.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 15:02:44 15.406u 0.342s 0:16.01 98.3% 0+0k 0+0io 0pf+0w