Sat Oct 15 14:37:35 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 14:37:35 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: HIT 107 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5791160 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): 1.288000 62.76100 ymin,ymax (A): 12.06000 58.85100 zmin,zma (A): -7.319000 42.26200 x,y,z range (A): 61.47300 46.79100 49.58100 scale (grids/A): 0.5791160 object centre (A): 32.02450 35.45550 17.47150 number of atom coordinates read : 2765 total number of charged atoms : 2627 net assigned charge : -0.4859756 assigned positive charge : 417.4893 centred at (gu) : 89.73214 89.95567 89.02290 assigned negative charge : -417.9763 centred at (gu) : 89.70924 90.14171 88.93565 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6063 nv = 96 ne = 84 npr = 55781 no. pairs analyzed = 55781 no. exposed pairs = 3504 no. arc points = 25048 no. surface atoms = 1179 nbur = 1586 mkacc time = 8.9999996E-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 = 1.512000 m= 280 mr = 3159 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2100000 number of dielectric boundary points 3165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2550 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7782 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3391411E-09 1.3116609E-09 midg,1,midg; midg,igrid,midg 3.6139545E-09 -3.8599666E-09 1,midg,midg; igrid,midg,midg -5.7633309E-10 3.5553582E-10 gauss-seidel spectral radius is 0.9845950 estimated iterations to convergence 66 setup time was (sec) 0.4700000 now iterating at: 14:37:36 rms-change max change #iterations 9.7968109E-02 14.90427 at 10iterations 7.3407125E-03 1.284020 at 20iterations 5.8244291E-04 9.3228698E-02 at 30iterations 4.5471490E-05 9.0701580E-03 at 40iterations 3.5331032E-06 6.1798096E-04 at 50iterations finished qdiffx linear iterations at : 14:37:44 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 3.5331032E-06 6.1798096E-04 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:37:45 4.240u 0.302s 0:10.75 42.2% 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 14:37:45 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: HIT 107 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: 1.737348 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): 1.288000 62.76100 ymin,ymax (A): 12.06000 58.85100 zmin,zma (A): -7.319000 42.26200 x,y,z range (A): 61.47300 46.79100 49.58100 scale (grids/A): 1.737348 object centre (A): 32.02450 35.45550 17.47150 number of atom coordinates read : 2765 total number of charged atoms : 2627 net assigned charge : -0.4859756 assigned positive charge : 417.4893 centred at (gu) : 89.19556 89.86643 87.06776 assigned negative charge : -417.9763 centred at (gu) : 89.12746 90.42461 86.80670 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25048 grid for indexing accessible points = 1.400000 m= 21395 mr = 45349 m= 2643 mr = 15063 m= 108 mr = 1404 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 0.3400000 number of dielectric boundary points 29273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20414 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) : 0.5791160 object centre at (A) : 32.02450 35.45550 17.47150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5473813E-03 2.0993915E-03 midg,1,midg; midg,igrid,midg 1.4235233E-02 -2.2402979E-02 1,midg,midg; igrid,midg,midg 7.1082604E-03 9.5530031E-03 gauss-seidel spectral radius is 0.9983799 estimated iterations to convergence 197 setup time was (sec) 0.5800000 now iterating at: 14:37:47 rms-change max change #iterations 3.661609 147.3944 at 10iterations 1.594728 62.04227 at 20iterations 0.6957414 22.84013 at 30iterations 0.3049735 10.45787 at 40iterations 0.1329265 4.499738 at 50iterations 5.7893466E-02 2.100960 at 60iterations 2.5317131E-02 0.9034958 at 70iterations 1.1123926E-02 0.3948364 at 80iterations 4.8623770E-03 0.1870384 at 90iterations 2.1244646E-03 7.7793598E-02 at 100iterations 9.3236606E-04 3.2817841E-02 at 110iterations 4.0809618E-04 1.4890432E-02 at 120iterations finished qdiffx linear iterations at : 14:38:05 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 4.0809618E-04 1.4890432E-02 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 14:38:06 8.646u 0.271s 0:20.26 43.9% 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 Sat Oct 15 2011 at 14:38:06 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: HIT 107 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: 2.606022 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): 1.288000 62.76100 ymin,ymax (A): 12.06000 58.85100 zmin,zma (A): -7.319000 42.26200 x,y,z range (A): 61.47300 46.79100 49.58100 scale (grids/A): 2.606022 object centre (A): 32.02450 35.45550 17.47150 number of atom coordinates read : 2765 total number of charged atoms : 2627 net assigned charge : -0.4859756 assigned positive charge : 417.4893 centred at (gu) : 88.79312 89.79925 85.60149 assigned negative charge : -417.9763 centred at (gu) : 88.69095 90.63680 85.20994 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 155191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25048 grid for indexing accessible points = 1.400000 m= 72525 mr = 110662 m= 22560 mr = 57926 m= 4306 mr = 17274 m= 443 mr = 3007 m= 21 mr = 290 m= 0 mr = 8 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2757 time to turn everything in is 0.8700000 number of dielectric boundary points 65879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 21009 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) : 1.737348 object centre at (A) : 32.02450 35.45550 17.47150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3445246E-02 1.8226629E-02 midg,1,midg; midg,igrid,midg 0.1930130 -0.2545965 1,midg,midg; igrid,midg,midg 0.1799833 0.2968957 gauss-seidel spectral radius is 0.9991955 estimated iterations to convergence 278 setup time was (sec) 1.160000 now iterating at: 14:38:08 rms-change max change #iterations 9.106939 370.5751 at 10iterations 5.167932 125.1594 at 20iterations 2.915141 64.67429 at 30iterations 1.642307 38.01140 at 40iterations 0.9224626 19.17468 at 50iterations 0.5184470 10.44419 at 60iterations 0.2906980 5.910938 at 70iterations 0.1630085 3.028183 at 80iterations 9.1463268E-02 1.793552 at 90iterations 5.1170133E-02 1.047644 at 100iterations 2.8652852E-02 0.7121811 at 110iterations 1.6059572E-02 0.3160443 at 120iterations 8.9855781E-03 0.1737099 at 130iterations 5.0314651E-03 0.1005135 at 140iterations 2.8206648E-03 6.0634613E-02 at 150iterations 1.5791729E-03 3.1604767E-02 at 160iterations 8.8184577E-04 1.7990112E-02 at 170iterations 4.9447839E-04 1.0072708E-02 at 180iterations finished qdiffx linear iterations at : 14:38:39 total time elapsed so far: 15.44000 # loops : 180 mean,max change (kT/e) : 4.9447839E-04 1.0072708E-02 energy calculations done at 15.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.57000 DelPhi exited at 14:38:40 15.573u 0.330s 0:34.01 46.7% 0+0k 0+0io 0pf+0w