Sat Oct 15 11:28:19 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 11:28:19 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 has a net charge of 1.4000 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: 0.6266282 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): -31.88300 17.52700 ymin,ymax (A): -23.65700 23.15500 zmin,zma (A): -12.39800 44.41400 x,y,z range (A): 49.41000 46.81200 56.81200 scale (grids/A): 0.6266282 object centre (A): -7.178000 -0.2510004 16.00800 number of atom coordinates read : 2597 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.59261 89.18445 89.83313 assigned negative charge : -390.0956 centred at (gu) : 88.48737 89.22642 89.72927 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6827 nv = 96 ne = 84 npr = 53356 no. pairs analyzed = 53356 no. exposed pairs = 3033 no. arc points = 21623 no. surface atoms = 1015 nbur = 1582 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3896 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 64 time to turn everything in is 0.1900000 number of dielectric boundary points 3243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2136 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8211 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0812602E-09 1.2359937E-08 midg,1,midg; midg,igrid,midg 9.4415160E-09 9.9210307E-10 1,midg,midg; igrid,midg,midg -5.6407887E-09 9.5320152E-09 gauss-seidel spectral radius is 0.9868074 estimated iterations to convergence 71 setup time was (sec) 0.4300000 now iterating at: 11:28:20 rms-change max change #iterations 0.1366068 22.87182 at 10iterations 1.2983357E-02 2.047562 at 20iterations 1.2368731E-03 0.1776276 at 30iterations 1.1515342E-04 1.5959740E-02 at 40iterations 1.1218202E-05 1.7013550E-03 at 50iterations finished qdiffx linear iterations at : 11:28:23 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 1.1218202E-05 1.7013550E-03 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 11:28:23 3.873u 0.239s 0:04.60 89.1% 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 Sat Oct 15 2011 at 11:28:24 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 has a net charge of 1.4000 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: 1.879884 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): -31.88300 17.52700 ymin,ymax (A): -23.65700 23.15500 zmin,zma (A): -12.39800 44.41400 x,y,z range (A): 49.41000 46.81200 56.81200 scale (grids/A): 1.879884 object centre (A): -7.178000 -0.2510004 16.00800 number of atom coordinates read : 2597 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 85.77747 87.55283 89.49889 assigned negative charge : -390.0956 centred at (gu) : 85.46174 87.67918 89.18771 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73727 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 27467 mr = 52165 m= 4006 mr = 20824 m= 200 mr = 2604 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4967 time to turn everything in is 0.3600000 number of dielectric boundary points 29745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19305 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) : 0.6266282 object centre at (A) : -7.178000 -0.2510004 16.00800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3294268E-02 3.1251464E-02 midg,1,midg; midg,igrid,midg 1.5479174E-02 3.7815024E-03 1,midg,midg; igrid,midg,midg -2.5065176E-03 3.9150998E-02 gauss-seidel spectral radius is 0.9985971 estimated iterations to convergence 212 setup time was (sec) 0.6000000 now iterating at: 11:28:25 rms-change max change #iterations 4.131447 192.8224 at 10iterations 1.916747 69.95871 at 20iterations 0.8861309 33.91325 at 30iterations 0.4109777 13.77331 at 40iterations 0.1908723 6.027933 at 50iterations 8.8693693E-02 2.899887 at 60iterations 4.1089021E-02 1.491155 at 70iterations 1.9028865E-02 0.6086998 at 80iterations 8.8442070E-03 0.2959557 at 90iterations 4.0920326E-03 0.1295757 at 100iterations 1.9021638E-03 5.9300900E-02 at 110iterations 8.8376092E-04 3.2714844E-02 at 120iterations finished qdiffx linear iterations at : 11:28:39 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 8.8376092E-04 3.2714844E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 11:28:40 8.133u 0.238s 0:16.43 50.8% 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 Sat Oct 15 2011 at 11:28:40 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 has a net charge of 1.4000 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: 2.819827 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): -31.88300 17.52700 ymin,ymax (A): -23.65700 23.15500 zmin,zma (A): -12.39800 44.41400 x,y,z range (A): 49.41000 46.81200 56.81200 scale (grids/A): 2.819827 object centre (A): -7.178000 -0.2510004 16.00800 number of atom coordinates read : 2597 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 83.66599 86.32934 89.24810 assigned negative charge : -390.0956 centred at (gu) : 83.19257 86.51876 88.78162 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 170334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 88925 mr = 125600 m= 32058 mr = 74532 m= 7175 mr = 26178 m= 862 mr = 5399 m= 55 mr = 571 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 17120 time to turn everything in is 0.9900000 number of dielectric boundary points 67105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 19726 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) : 1.879884 object centre at (A) : -7.178000 -0.2510004 16.00800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1561925 0.4240009 midg,1,midg; midg,igrid,midg 0.1799312 3.1004112E-02 1,midg,midg; igrid,midg,midg -2.7587335E-03 0.4928206 gauss-seidel spectral radius is 0.9992408 estimated iterations to convergence 286 setup time was (sec) 1.280000 now iterating at: 11:28:42 rms-change max change #iterations 9.691580 319.5397 at 10iterations 5.585348 108.1348 at 20iterations 3.193527 73.43127 at 30iterations 1.828564 43.46413 at 40iterations 1.044775 25.71457 at 50iterations 0.5951087 11.62639 at 60iterations 0.3403827 6.063278 at 70iterations 0.1940745 3.653492 at 80iterations 0.1107293 2.089257 at 90iterations 6.3172042E-02 1.177681 at 100iterations 3.6154710E-02 0.6704178 at 110iterations 2.0591769E-02 0.4196014 at 120iterations 1.1736530E-02 0.2158689 at 130iterations 6.6724638E-03 0.1241150 at 140iterations 3.8041475E-03 6.7655563E-02 at 150iterations 2.1702251E-03 3.9778709E-02 at 160iterations 1.2365420E-03 2.6773453E-02 at 170iterations 7.0683792E-04 1.3560295E-02 at 180iterations finished qdiffx linear iterations at : 11:28:54 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 7.0683792E-04 1.3560295E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.63000 DelPhi exited at 11:28:55 13.627u 0.370s 0:14.62 95.6% 0+0k 0+0io 0pf+0w