Mon Oct 10 09:20:58 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 Mon Oct 10 2011 at 09:20:58 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2889 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5406556 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): -43.53900 22.30700 ymin,ymax (A): 109.6150 164.1620 zmin,zma (A): 155.1770 207.2610 x,y,z range (A): 65.84599 54.54700 52.08400 scale (grids/A): 0.5406556 object centre (A): -10.61600 136.8885 181.2190 number of atom coordinates read : 2889 total number of charged atoms : 2737 net assigned charge : 5.014013 assigned positive charge : 422.8958 centred at (gu) : 88.40267 89.65788 87.01719 assigned negative charge : -417.8823 centred at (gu) : 88.29167 89.59904 86.92956 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5679 nv = 96 ne = 84 npr = 56385 no. pairs analyzed = 56385 no. exposed pairs = 4397 no. arc points = 31930 no. surface atoms = 1445 nbur = 1444 mkacc time = 9.9999994E-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 = 1.596000 m= 212 mr = 2453 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3132 ## 427 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7377 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8614553E-10 3.4209230E-10 midg,1,midg; midg,igrid,midg -2.5108336E-11 5.2279470E-10 1,midg,midg; igrid,midg,midg -4.4387130E-10 5.5569227E-10 gauss-seidel spectral radius is 0.9823737 estimated iterations to convergence 62 setup time was (sec) 0.4100000 now iterating at: 09:20:59 rms-change max change #iterations 6.8228051E-02 11.64770 at 10iterations 4.4219564E-03 0.7893476 at 20iterations 2.9830268E-04 6.1809540E-02 at 30iterations 2.8924502E-05 4.7531128E-03 at 40iterations 5.1431130E-06 6.4468384E-04 at 50iterations finished qdiffx linear iterations at : 09:21:01 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.1431130E-06 6.4468384E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 09:21:02 3.438u 0.171s 0:03.94 91.3% 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 09:21:02 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2889 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.621967 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): -43.53900 22.30700 ymin,ymax (A): 109.6150 164.1620 zmin,zma (A): 155.1770 207.2610 x,y,z range (A): 65.84599 54.54700 52.08400 scale (grids/A): 1.621967 object centre (A): -10.61600 136.8885 181.2190 number of atom coordinates read : 2889 total number of charged atoms : 2737 net assigned charge : 5.014013 assigned positive charge : 422.8958 centred at (gu) : 85.20728 88.97334 81.05138 assigned negative charge : -417.8823 centred at (gu) : 84.87487 88.79689 80.78835 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31930 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18342 mr = 37463 m= 1797 mr = 11361 m= 55 mr = 604 m= 3 mr = 1 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 0.3100000 number of dielectric boundary points 31986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 20991 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) : 0.5406556 object centre at (A) : -10.61600 136.8885 181.2190 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8171972E-03 3.3877157E-03 midg,1,midg; midg,igrid,midg -4.1346140E-03 1.4504240E-02 1,midg,midg; igrid,midg,midg -1.3014754E-02 1.5436218E-02 gauss-seidel spectral radius is 0.9981640 estimated iterations to convergence 185 setup time was (sec) 0.5200000 now iterating at: 09:21:03 rms-change max change #iterations 3.144214 160.9016 at 10iterations 1.297544 52.20434 at 20iterations 0.5337920 23.74454 at 30iterations 0.2209639 8.257652 at 40iterations 9.1535449E-02 3.671891 at 50iterations 3.7721399E-02 1.566227 at 60iterations 1.5666734E-02 0.6483955 at 70iterations 6.4706001E-03 0.2465019 at 80iterations 2.6896705E-03 0.1022873 at 90iterations 1.1108069E-03 4.7919273E-02 at 100iterations 4.6371820E-04 1.8427610E-02 at 110iterations 1.9332588E-04 7.4462891E-03 at 120iterations finished qdiffx linear iterations at : 09:21:10 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.9332588E-04 7.4462891E-03 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 09:21:10 7.707u 0.212s 0:08.18 96.6% 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 Mon Oct 10 2011 at 09:21:10 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2889 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.432950 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): -43.53900 22.30700 ymin,ymax (A): 109.6150 164.1620 zmin,zma (A): 155.1770 207.2610 x,y,z range (A): 65.84599 54.54700 52.08400 scale (grids/A): 2.432950 object centre (A): -10.61600 136.8885 181.2190 number of atom coordinates read : 2889 total number of charged atoms : 2737 net assigned charge : 5.014013 assigned positive charge : 422.8958 centred at (gu) : 82.81066 88.45998 76.57693 assigned negative charge : -417.8823 centred at (gu) : 82.31210 88.19515 76.18237 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 141806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31930 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 62156 mr = 92913 m= 17476 mr = 45819 m= 2522 mr = 11933 m= 157 mr = 1249 m= 4 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 72178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21865 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) : 1.621967 object centre at (A) : -10.61600 136.8885 181.2190 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6290515E-02 4.1385688E-02 midg,1,midg; midg,igrid,midg -0.1516021 0.2859374 1,midg,midg; igrid,midg,midg -0.4690346 0.6038514 gauss-seidel spectral radius is 0.9991383 estimated iterations to convergence 269 setup time was (sec) 1.000000 now iterating at: 09:21:11 rms-change max change #iterations 8.487702 328.7122 at 10iterations 4.867072 183.6021 at 20iterations 2.749576 87.51768 at 30iterations 1.545732 51.61572 at 40iterations 0.8643119 26.72252 at 50iterations 0.4813362 12.62346 at 60iterations 0.2672700 6.732758 at 70iterations 0.1479196 4.011875 at 80iterations 8.1818372E-02 2.105492 at 90iterations 4.5248792E-02 1.117695 at 100iterations 2.4946725E-02 0.6210098 at 110iterations 1.3745974E-02 0.3125272 at 120iterations 7.5722602E-03 0.2049870 at 130iterations 4.1741044E-03 0.1011295 at 140iterations 2.2943332E-03 5.9129953E-02 at 150iterations 1.2594202E-03 3.0269623E-02 at 160iterations 6.9435337E-04 1.5908241E-02 at 170iterations 3.8239712E-04 8.9340210E-03 at 180iterations finished qdiffx linear iterations at : 09:21:23 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 3.8239712E-04 8.9340210E-03 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 09:21:23 12.340u 0.201s 0:12.80 97.9% 0+0k 0+0io 0pf+0w