Sat Oct 8 13:46:05 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 13:46:05 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6501570 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): -12.21800 42.53800 ymin,ymax (A): -22.38200 22.58400 zmin,zma (A): -6.360000 48.16300 x,y,z range (A): 54.75600 44.96600 54.52300 scale (grids/A): 0.6501570 object centre (A): 15.16000 0.1009998 20.90150 number of atom coordinates read : 3003 total number of charged atoms : 2857 net assigned charge : -0.9859914 assigned positive charge : 450.2016 centred at (gu) : 89.09774 89.61066 91.17319 assigned negative charge : -451.1883 centred at (gu) : 89.14564 89.48864 91.10585 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8589 nv = 96 ne = 84 npr = 61845 no. pairs analyzed = 61845 no. exposed pairs = 3515 no. arc points = 24238 no. surface atoms = 1187 nbur = 1816 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 514 mr = 5079 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3300000 number of dielectric boundary points 3964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2369 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10281 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0987544E-08 1.2729170E-08 midg,1,midg; midg,igrid,midg -2.6108445E-08 1.7806483E-08 1,midg,midg; igrid,midg,midg 7.8423072E-09 -8.7498941E-09 gauss-seidel spectral radius is 0.9877751 estimated iterations to convergence 74 setup time was (sec) 0.5500000 now iterating at: 13:46:05 rms-change max change #iterations 0.1749309 21.60569 at 10iterations 1.7979512E-02 2.872025 at 20iterations 1.8707310E-03 0.2412643 at 30iterations 2.1279039E-04 3.2402039E-02 at 40iterations 3.0012041E-05 3.7388802E-03 at 50iterations finished qdiffx linear iterations at : 13:46:08 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 3.0012041E-05 3.7388802E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 13:46:08 3.147u 0.131s 0:03.59 91.0% 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 13:46:08 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.950471 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): -12.21800 42.53800 ymin,ymax (A): -22.38200 22.58400 zmin,zma (A): -6.360000 48.16300 x,y,z range (A): 54.75600 44.96600 54.52300 scale (grids/A): 1.950471 object centre (A): 15.16000 0.1009998 20.90150 number of atom coordinates read : 3003 total number of charged atoms : 2857 net assigned charge : -0.9859914 assigned positive charge : 450.2016 centred at (gu) : 87.29273 88.83138 93.51894 assigned negative charge : -451.1883 centred at (gu) : 87.43678 88.46555 93.31736 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 93768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24238 grid for indexing accessible points = 1.400000 m= 36105 mr = 67983 m= 6006 mr = 27730 m= 363 mr = 3867 m= 5 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 36545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22558 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) : 0.6501570 object centre at (A) : 15.16000 0.1009998 20.90150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9026173E-02 2.2961581E-02 midg,1,midg; midg,igrid,midg -8.9748334E-03 2.2176830E-02 1,midg,midg; igrid,midg,midg -1.3311611E-02 -4.0191128E-03 gauss-seidel spectral radius is 0.9987326 estimated iterations to convergence 222 setup time was (sec) 0.9000000 now iterating at: 13:46:09 rms-change max change #iterations 4.854794 183.5261 at 10iterations 2.350382 65.28117 at 20iterations 1.129015 35.90418 at 30iterations 0.5469921 17.71978 at 40iterations 0.2635805 8.281007 at 50iterations 0.1271275 3.652489 at 60iterations 6.1270997E-02 1.740786 at 70iterations 2.9562039E-02 0.8457718 at 80iterations 1.4293589E-02 0.3647289 at 90iterations 6.9095716E-03 0.2173100 at 100iterations 3.3387740E-03 9.4524145E-02 at 110iterations 1.6209474E-03 4.2758942E-02 at 120iterations finished qdiffx linear iterations at : 13:46:16 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 1.6209474E-03 4.2758942E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 13:46:16 7.354u 0.159s 0:07.80 96.1% 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 8 2011 at 13:46:16 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.925707 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): -12.21800 42.53800 ymin,ymax (A): -22.38200 22.58400 zmin,zma (A): -6.360000 48.16300 x,y,z range (A): 54.75600 44.96600 54.52300 scale (grids/A): 2.925707 object centre (A): 15.16000 0.1009998 20.90150 number of atom coordinates read : 3003 total number of charged atoms : 2857 net assigned charge : -0.9859914 assigned positive charge : 450.2016 centred at (gu) : 85.93873 88.24704 95.27814 assigned negative charge : -451.1883 centred at (gu) : 86.15516 87.69830 94.97597 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 216846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24238 grid for indexing accessible points = 1.400000 m= 115757 mr = 164021 m= 44059 mr = 97143 m= 11001 mr = 36322 m= 1555 mr = 8321 m= 78 mr = 1032 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 82441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 22852 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) : 1.950471 object centre at (A) : 15.16000 0.1009998 20.90150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2671793E-02 0.3095659 midg,1,midg; midg,igrid,midg -5.2605558E-02 0.2491519 1,midg,midg; igrid,midg,midg -3.0247923E-02 0.1220001 gauss-seidel spectral radius is 0.9992880 estimated iterations to convergence 296 setup time was (sec) 1.910000 now iterating at: 13:46:18 rms-change max change #iterations 11.20763 495.5793 at 10iterations 6.608214 136.2460 at 20iterations 3.889025 66.53842 at 30iterations 2.276518 39.15642 at 40iterations 1.335215 22.16892 at 50iterations 0.7810327 14.25227 at 60iterations 0.4557655 8.223036 at 70iterations 0.2657045 4.184532 at 80iterations 0.1549116 2.484192 at 90iterations 9.0142950E-02 1.550642 at 100iterations 5.2559812E-02 0.8948109 at 110iterations 3.0556960E-02 0.5036659 at 120iterations 1.7786982E-02 0.2801767 at 130iterations 1.0345661E-02 0.1751447 at 140iterations 6.0260049E-03 8.9981079E-02 at 150iterations 3.5026241E-03 5.7942390E-02 at 160iterations 2.0428461E-03 3.1845093E-02 at 170iterations 1.1937877E-03 1.9228339E-02 at 180iterations finished qdiffx linear iterations at : 13:46:28 total time elapsed so far: 11.58000 # loops : 180 mean,max change (kT/e) : 1.1937877E-03 1.9228339E-02 energy calculations done at 11.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 13:46:28 11.756u 0.162s 0:12.22 97.4% 0+0k 0+0io 0pf+0w