Tue Oct 11 00:21:20 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 00:21:20 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 !!! WARNING: GLM 762 has a net charge of -0.0940 !!! WARNING: HIR 1025 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5195867 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): -21.04100 40.58000 ymin,ymax (A): 10.20000 75.58000 zmin,zma (A): -15.28200 53.23400 x,y,z range (A): 61.62100 65.38000 68.51600 scale (grids/A): 0.5195867 object centre (A): 9.769501 42.89000 18.97600 number of atom coordinates read : 3958 total number of charged atoms : 3803 net assigned charge : 9.920044 assigned positive charge : 611.7077 centred at (gu) : 91.13867 89.95061 91.66626 assigned negative charge : -601.7897 centred at (gu) : 91.18439 90.09845 91.62943 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6757 nv = 96 ne = 84 npr = 77668 no. pairs analyzed = 77668 no. exposed pairs = 5117 no. arc points = 35727 no. surface atoms = 1717 nbur = 2241 mkacc time = 0.1700000 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 = 1.652000 m= 226 mr = 3318 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3700000 number of dielectric boundary points 3662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3636 ## 588 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9139 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1005499E-11 4.9835630E-10 midg,1,midg; midg,igrid,midg 6.7634903E-10 -2.6710112E-10 1,midg,midg; igrid,midg,midg 2.6327010E-10 7.9626979E-11 gauss-seidel spectral radius is 0.9809985 estimated iterations to convergence 60 setup time was (sec) 0.6100000 now iterating at: 00:21:21 rms-change max change #iterations 6.9626071E-02 10.89799 at 10iterations 5.1226630E-03 1.015301 at 20iterations 7.6759682E-04 0.1997108 at 30iterations 1.6911674E-04 4.6787262E-02 at 40iterations 3.9249924E-05 1.0959625E-02 at 50iterations finished qdiffx linear iterations at : 00:21:23 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 3.9249924E-05 1.0959625E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 00:21:24 3.403u 0.167s 0:03.92 90.8% 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 00:21:24 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 !!! WARNING: GLM 762 has a net charge of -0.0940 !!! WARNING: HIR 1025 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.558760 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): -21.04100 40.58000 ymin,ymax (A): 10.20000 75.58000 zmin,zma (A): -15.28200 53.23400 x,y,z range (A): 61.62100 65.38000 68.51600 scale (grids/A): 1.558760 object centre (A): 9.769501 42.89000 18.97600 number of atom coordinates read : 3958 total number of charged atoms : 3803 net assigned charge : 9.920044 assigned positive charge : 611.7077 centred at (gu) : 93.41460 89.85133 94.99774 assigned negative charge : -601.7897 centred at (gu) : 93.55274 90.29487 94.88776 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35727 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 21249 mr = 50528 m= 1669 mr = 13812 m= 29 mr = 646 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1190 time to turn everything in is 0.5500000 number of dielectric boundary points 34066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 469 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 28735 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) : 0.5195867 object centre at (A) : 9.769501 42.89000 18.97600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0486115E-02 6.7057423E-03 midg,1,midg; midg,igrid,midg 2.1568127E-02 1.3121486E-02 1,midg,midg; igrid,midg,midg 3.1251090E-03 1.6431561E-02 gauss-seidel spectral radius is 0.9980910 estimated iterations to convergence 182 setup time was (sec) 0.8400000 now iterating at: 00:21:25 rms-change max change #iterations 3.581196 147.5061 at 10iterations 1.455001 51.08060 at 20iterations 0.5907917 21.73064 at 30iterations 0.2417060 8.966289 at 40iterations 9.8832801E-02 3.456421 at 50iterations 4.0420815E-02 1.375547 at 60iterations 1.6597925E-02 0.5983562 at 70iterations 6.8792296E-03 0.2528934 at 80iterations 2.9236497E-03 0.1018200 at 90iterations 1.2987984E-03 5.2824020E-02 at 100iterations 6.0076197E-04 2.8448105E-02 at 110iterations 3.0212494E-04 1.6139984E-02 at 120iterations finished qdiffx linear iterations at : 00:21:32 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 3.0212494E-04 1.6139984E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 00:21:32 7.477u 0.209s 0:08.24 93.0% 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 Tue Oct 11 2011 at 00:21:32 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 !!! WARNING: GLM 762 has a net charge of -0.0940 !!! WARNING: HIR 1025 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.338140 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): -21.04100 40.58000 ymin,ymax (A): 10.20000 75.58000 zmin,zma (A): -15.28200 53.23400 x,y,z range (A): 61.62100 65.38000 68.51600 scale (grids/A): 2.338140 object centre (A): 9.769501 42.89000 18.97600 number of atom coordinates read : 3958 total number of charged atoms : 3803 net assigned charge : 9.920044 assigned positive charge : 611.7077 centred at (gu) : 95.12186 89.77666 97.49632 assigned negative charge : -601.7897 centred at (gu) : 95.32912 90.44217 97.33151 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 177223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35727 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 76122 mr = 124427 m= 18776 mr = 58469 m= 2374 mr = 13490 m= 84 mr = 1303 m= 0 mr = 24 time to grow re-entrant surface = 0.6900000 no. cavity mid-points inaccessible to solvent = 3985 time to turn everything in is 1.260000 number of dielectric boundary points 76866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 30362 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) : 1.558760 object centre at (A) : 9.769501 42.89000 18.97600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2593156 0.1092927 midg,1,midg; midg,igrid,midg 0.3106719 0.2256789 1,midg,midg; igrid,midg,midg 8.4704727E-02 0.3018091 gauss-seidel spectral radius is 0.9991271 estimated iterations to convergence 267 setup time was (sec) 1.570000 now iterating at: 00:21:34 rms-change max change #iterations 9.586917 362.1868 at 10iterations 5.391881 138.5831 at 20iterations 3.011224 73.47074 at 30iterations 1.674628 36.66617 at 40iterations 0.9274776 19.42427 at 50iterations 0.5133727 11.55633 at 60iterations 0.2827780 6.318548 at 70iterations 0.1555856 3.231529 at 80iterations 8.5536793E-02 1.756823 at 90iterations 4.7053240E-02 0.8866158 at 100iterations 2.5890484E-02 0.5278454 at 110iterations 1.4238450E-02 0.2723508 at 120iterations 7.8295032E-03 0.1586800 at 130iterations 4.3225186E-03 9.0675354E-02 at 140iterations 2.4012059E-03 4.9514771E-02 at 150iterations 1.3433984E-03 3.0536652E-02 at 160iterations 7.6213857E-04 1.8745422E-02 at 170iterations 4.4249734E-04 1.0791779E-02 at 180iterations finished qdiffx linear iterations at : 00:21:45 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 4.4249734E-04 1.0791779E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 00:21:45 12.626u 0.213s 0:13.13 97.7% 0+0k 0+0io 0pf+0w