Sat Oct 15 14:28:12 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 14:28:12 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2957 !!! WARNING: HIR 148 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: 0.5443258 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): -1.156000 64.24600 ymin,ymax (A): 11.82500 58.35200 zmin,zma (A): -6.696000 38.82700 x,y,z range (A): 65.40200 46.52700 45.52300 scale (grids/A): 0.5443258 object centre (A): 31.54500 35.08850 16.06550 number of atom coordinates read : 2957 total number of charged atoms : 2816 net assigned charge : -2.985976 assigned positive charge : 445.4250 centred at (gu) : 89.13778 89.95377 89.61293 assigned negative charge : -448.4121 centred at (gu) : 89.09362 90.10719 89.51258 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5570 nv = 96 ne = 84 npr = 59357 no. pairs analyzed = 59357 no. exposed pairs = 3902 no. arc points = 27343 no. surface atoms = 1303 nbur = 1654 mkacc time = 0.1000000 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= 253 mr = 2785 m= 0 mr = 5 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2700 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7381 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9036467E-10 4.1286255E-10 midg,1,midg; midg,igrid,midg 7.8886014E-10 -1.1398353E-09 1,midg,midg; igrid,midg,midg -5.5503629E-10 8.5953127E-11 gauss-seidel spectral radius is 0.9826009 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 14:28:13 rms-change max change #iterations 7.3930450E-02 14.89745 at 10iterations 4.8710559E-03 0.7867508 at 20iterations 3.1593980E-04 4.8808098E-02 at 30iterations 2.1422356E-05 3.6621094E-03 at 40iterations 1.3985907E-06 2.1743774E-04 at 50iterations finished qdiffx linear iterations at : 14:28:16 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.3985907E-06 2.1743774E-04 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 14:28:16 3.640u 0.206s 0:04.12 93.2% 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 14:28:16 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2957 !!! WARNING: HIR 148 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: 1.632978 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): -1.156000 64.24600 ymin,ymax (A): 11.82500 58.35200 zmin,zma (A): -6.696000 38.82700 x,y,z range (A): 65.40200 46.52700 45.52300 scale (grids/A): 1.632978 object centre (A): 31.54500 35.08850 16.06550 number of atom coordinates read : 2957 total number of charged atoms : 2816 net assigned charge : -2.985976 assigned positive charge : 445.4250 centred at (gu) : 87.41224 89.86059 88.83809 assigned negative charge : -448.4121 centred at (gu) : 87.28041 90.32143 88.53709 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62017 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27343 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17852 mr = 40772 m= 1669 mr = 11750 m= 39 mr = 740 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 602 time to turn everything in is 0.3100000 number of dielectric boundary points 28315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21601 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) : 0.5443258 object centre at (A) : 31.54500 35.08850 16.06550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5325384E-03 2.6252070E-03 midg,1,midg; midg,igrid,midg 7.6458142E-03 -1.6895510E-02 1,midg,midg; igrid,midg,midg -2.4405386E-02 -3.9893994E-03 gauss-seidel spectral radius is 0.9981807 estimated iterations to convergence 186 setup time was (sec) 0.5200000 now iterating at: 14:28:17 rms-change max change #iterations 3.338013 190.3946 at 10iterations 1.379662 72.21185 at 20iterations 0.5742526 23.20001 at 30iterations 0.2392087 8.277988 at 40iterations 9.9193938E-02 3.711184 at 50iterations 4.1248299E-02 1.436563 at 60iterations 1.7226733E-02 0.6080599 at 70iterations 7.1781562E-03 0.2841663 at 80iterations 2.9723083E-03 0.1085367 at 90iterations 1.2424664E-03 4.4982910E-02 at 100iterations 5.1714899E-04 1.8893003E-02 at 110iterations 2.1569710E-04 7.5454712E-03 at 120iterations finished qdiffx linear iterations at : 14:28:31 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.1569710E-04 7.5454712E-03 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 14:28:32 7.895u 0.227s 0:15.32 52.9% 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 14:28:32 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2957 !!! WARNING: HIR 148 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: 2.449466 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): -1.156000 64.24600 ymin,ymax (A): 11.82500 58.35200 zmin,zma (A): -6.696000 38.82700 x,y,z range (A): 65.40200 46.52700 45.52300 scale (grids/A): 2.449466 object centre (A): 31.54500 35.08850 16.06550 number of atom coordinates read : 2957 total number of charged atoms : 2816 net assigned charge : -2.985976 assigned positive charge : 445.4250 centred at (gu) : 86.11816 89.79066 88.25689 assigned negative charge : -448.4121 centred at (gu) : 85.92065 90.48206 87.80547 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 144370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27343 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 62515 mr = 100595 m= 16836 mr = 48128 m= 2407 mr = 12195 m= 139 mr = 1515 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1921 time to turn everything in is 0.7400000 number of dielectric boundary points 63781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22504 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) : 1.632978 object centre at (A) : 31.54500 35.08850 16.06550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9119882E-02 3.2212269E-02 midg,1,midg; midg,igrid,midg 0.1315118 -0.2292919 1,midg,midg; igrid,midg,midg -0.7513591 0.1030980 gauss-seidel spectral radius is 0.9991391 estimated iterations to convergence 269 setup time was (sec) 0.9900000 now iterating at: 14:28:33 rms-change max change #iterations 8.716552 319.5723 at 10iterations 4.865931 135.3920 at 20iterations 2.708791 61.13955 at 30iterations 1.503485 40.00511 at 40iterations 0.8306087 17.93042 at 50iterations 0.4572035 10.31956 at 60iterations 0.2519693 5.206669 at 70iterations 0.1384559 2.924038 at 80iterations 7.6112904E-02 1.620795 at 90iterations 4.1953951E-02 0.8975220 at 100iterations 2.3007944E-02 0.4712696 at 110iterations 1.2634901E-02 0.2786469 at 120iterations 6.9272197E-03 0.1344271 at 130iterations 3.8058206E-03 8.1432343E-02 at 140iterations 2.0869013E-03 4.2795181E-02 at 150iterations 1.1453070E-03 2.3744401E-02 at 160iterations 6.2944734E-04 1.4172435E-02 at 170iterations 3.4598284E-04 7.3680878E-03 at 180iterations finished qdiffx linear iterations at : 14:28:56 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 3.4598284E-04 7.3680878E-03 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 14:28:57 12.749u 0.239s 0:25.17 51.5% 0+0k 0+0io 0pf+0w