Sat Oct 8 14:45:33 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 8 2011 at 14:45:33 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6386796 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): -12.18400 43.55600 ymin,ymax (A): -23.01000 22.40600 zmin,zma (A): -6.631000 47.83100 x,y,z range (A): 55.74000 45.41600 54.46200 scale (grids/A): 0.6386796 object centre (A): 15.68600 -0.3020000 20.60000 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.985993 assigned positive charge : 455.5896 centred at (gu) : 88.83259 89.85614 91.22829 assigned negative charge : -457.5762 centred at (gu) : 88.79300 89.75666 91.19596 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8212 nv = 96 ne = 84 npr = 63548 no. pairs analyzed = 63548 no. exposed pairs = 3450 no. arc points = 24304 no. surface atoms = 1176 nbur = 1858 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 4770 m= 0 mr = 38 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2365 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4132188E-09 2.0520752E-09 midg,1,midg; midg,igrid,midg -1.6548517E-08 9.9584323E-09 1,midg,midg; igrid,midg,midg -1.0291446E-08 1.8938715E-09 gauss-seidel spectral radius is 0.9873321 estimated iterations to convergence 73 setup time was (sec) 0.7100000 now iterating at: 14:45:34 rms-change max change #iterations 0.1547786 21.16380 at 10iterations 1.5357066E-02 2.206921 at 20iterations 1.5922465E-03 0.2154136 at 30iterations 1.6260290E-04 1.9596100E-02 at 40iterations 1.8721839E-05 2.4609566E-03 at 50iterations finished qdiffx linear iterations at : 14:45:38 total time elapsed so far: 5.190000 # loops : 50 mean,max change (kT/e) : 1.8721839E-05 2.4609566E-03 energy calculations done at 5.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.360000 DelPhi exited at 14:45:39 5.364u 0.482s 0:06.19 94.3% 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 Sat Oct 8 2011 at 14:45:39 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.916039 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): -12.18400 43.55600 ymin,ymax (A): -23.01000 22.40600 zmin,zma (A): -6.631000 47.83100 x,y,z range (A): 55.74000 45.41600 54.46200 scale (grids/A): 1.916039 object centre (A): 15.68600 -0.3020000 20.60000 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.985993 assigned positive charge : 455.5896 centred at (gu) : 86.49718 89.56795 93.68403 assigned negative charge : -457.5762 centred at (gu) : 86.37886 89.26970 93.58734 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24304 grid for indexing accessible points = 1.400000 m= 32289 mr = 64823 m= 4594 mr = 24165 m= 271 mr = 2745 m= 7 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.7500000 number of dielectric boundary points 35091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 22749 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) : 0.6386796 object centre at (A) : 15.68600 -0.3020000 20.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2334684E-02 3.4071030E-03 midg,1,midg; midg,igrid,midg -9.2281094E-03 1.6974725E-02 1,midg,midg; igrid,midg,midg -3.8070314E-02 1.2342983E-02 gauss-seidel spectral radius is 0.9986863 estimated iterations to convergence 219 setup time was (sec) 1.120000 now iterating at: 14:45:40 rms-change max change #iterations 4.689907 212.2110 at 10iterations 2.234444 72.78798 at 20iterations 1.060733 32.95530 at 30iterations 0.5051765 14.12425 at 40iterations 0.2408929 6.998788 at 50iterations 0.1146161 3.257515 at 60iterations 5.4470375E-02 1.622526 at 70iterations 2.5897603E-02 0.6881838 at 80iterations 1.2348679E-02 0.3364713 at 90iterations 5.8622151E-03 0.1690046 at 100iterations 2.7957186E-03 7.6272011E-02 at 110iterations 1.3338582E-03 3.9555550E-02 at 120iterations finished qdiffx linear iterations at : 14:45:52 total time elapsed so far: 12.84000 # loops : 120 mean,max change (kT/e) : 1.3338582E-03 3.9555550E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 14:45:53 13.030u 0.519s 0:13.81 98.0% 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 Sat Oct 8 2011 at 14:45:53 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.874058 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): -12.18400 43.55600 ymin,ymax (A): -23.01000 22.40600 zmin,zma (A): -6.631000 47.83100 x,y,z range (A): 55.74000 45.41600 54.46200 scale (grids/A): 2.874058 object centre (A): 15.68600 -0.3020000 20.60000 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.985993 assigned positive charge : 455.5896 centred at (gu) : 84.74565 89.35168 95.52584 assigned negative charge : -457.5762 centred at (gu) : 84.56828 88.90446 95.38097 start vw surface at 0.1300000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 207702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24304 grid for indexing accessible points = 1.400000 m= 106052 mr = 156329 m= 36821 mr = 88323 m= 8223 mr = 29533 m= 1139 mr = 5938 m= 70 mr = 756 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 549 time to turn everything in is 1.960000 number of dielectric boundary points 79103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 23096 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) : 1.916039 object centre at (A) : 15.68600 -0.3020000 20.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1473789E-02 0.1642779 midg,1,midg; midg,igrid,midg -7.8492798E-02 0.1977561 1,midg,midg; igrid,midg,midg -0.5602171 0.1820377 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 2.360000 now iterating at: 14:45:56 rms-change max change #iterations 11.04200 406.9611 at 10iterations 6.489542 125.6455 at 20iterations 3.785692 85.54319 at 30iterations 2.210710 42.02364 at 40iterations 1.284347 22.54695 at 50iterations 0.7471594 13.39000 at 60iterations 0.4338246 7.387421 at 70iterations 0.2515870 4.652208 at 80iterations 0.1459134 2.627048 at 90iterations 8.4681109E-02 1.432273 at 100iterations 4.8943616E-02 0.8198862 at 110iterations 2.8316181E-02 0.4666734 at 120iterations 1.6407222E-02 0.2615051 at 130iterations 9.5043005E-03 0.1559143 at 140iterations 5.4939929E-03 8.8354111E-02 at 150iterations 3.1785811E-03 5.3322494E-02 at 160iterations 1.8400939E-03 3.5160542E-02 at 170iterations 1.0677770E-03 1.9983292E-02 at 180iterations finished qdiffx linear iterations at : 14:46:15 total time elapsed so far: 22.07000 # loops : 180 mean,max change (kT/e) : 1.0677770E-03 1.9983292E-02 energy calculations done at 22.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.24000 DelPhi exited at 14:46:16 22.243u 0.571s 0:23.12 98.6% 0+0k 0+0io 0pf+0w