Sun Oct 9 17:51:28 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 Sun Oct 9 2011 at 17:51:28 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5232 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5490862 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): 3.278000 68.11300 ymin,ymax (A): -8.778000 53.34100 zmin,zma (A): -0.8030000 63.47700 x,y,z range (A): 64.83500 62.11900 64.28000 scale (grids/A): 0.5490862 object centre (A): 35.69550 22.28150 31.33700 number of atom coordinates read : 5232 total number of charged atoms : 5085 net assigned charge : 1.635045 assigned positive charge : 806.7024 centred at (gu) : 88.11012 89.14745 89.03326 assigned negative charge : -805.0735 centred at (gu) : 87.96017 89.18507 88.98758 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 10213 nv = 96 ne = 84 npr = 106228 no. pairs analyzed = 106228 no. exposed pairs = 6134 no. arc points = 41234 no. surface atoms = 2094 nbur = 3138 mkacc time = 0.2500000 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 = 1.568000 m= 464 mr = 5807 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4256 ## 485 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 13535 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8337346E-10 6.0578809E-10 midg,1,midg; midg,igrid,midg 8.1964147E-10 -2.7936414E-10 1,midg,midg; igrid,midg,midg -3.0555580E-09 1.3384760E-09 gauss-seidel spectral radius is 0.9830595 estimated iterations to convergence 63 setup time was (sec) 0.7700000 now iterating at: 17:51:29 rms-change max change #iterations 0.1067292 14.04857 at 10iterations 9.6797645E-03 1.417427 at 20iterations 2.8559053E-03 0.3265228 at 30iterations 1.3033435E-03 0.1660666 at 40iterations 6.1593141E-04 8.2528591E-02 at 50iterations finished qdiffx linear iterations at : 17:51:32 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 6.1593141E-04 8.2528591E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 17:51:33 3.645u 0.144s 0:04.07 92.8% 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 Sun Oct 9 2011 at 17:51:33 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5232 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.647258 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): 3.278000 68.11300 ymin,ymax (A): -8.778000 53.34100 zmin,zma (A): -0.8030000 63.47700 x,y,z range (A): 64.83500 62.11900 64.28000 scale (grids/A): 1.647258 object centre (A): 35.69550 22.28150 31.33700 number of atom coordinates read : 5232 total number of charged atoms : 5085 net assigned charge : 1.635045 assigned positive charge : 806.7024 centred at (gu) : 84.32906 87.44113 87.09855 assigned negative charge : -805.0735 centred at (gu) : 83.88009 87.55495 86.96275 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 114451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41234 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39258 mr = 82921 m= 4748 mr = 28185 m= 151 mr = 2503 m= 0 mr = 19 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 44980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 39003 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) : 0.5490862 object centre at (A) : 35.69550 22.28150 31.33700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0007783E-02 -6.9045294E-03 midg,1,midg; midg,igrid,midg 2.0346256E-02 8.1391605E-03 1,midg,midg; igrid,midg,midg -3.2275639E-02 1.7432697E-02 gauss-seidel spectral radius is 0.9984199 estimated iterations to convergence 200 setup time was (sec) 1.150000 now iterating at: 17:51:34 rms-change max change #iterations 4.855968 178.3014 at 10iterations 2.147847 64.73450 at 20iterations 0.9501701 26.19016 at 30iterations 0.4217563 11.69144 at 40iterations 0.1869403 5.023436 at 50iterations 8.3348021E-02 2.263628 at 60iterations 3.7518080E-02 1.134247 at 70iterations 1.7245570E-02 0.4811640 at 80iterations 8.4069995E-03 0.2452621 at 90iterations 4.5490004E-03 0.1231766 at 100iterations 2.8344223E-03 7.3883057E-02 at 110iterations 1.9688183E-03 5.4077148E-02 at 120iterations finished qdiffx linear iterations at : 17:51:40 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.9688183E-03 5.4077148E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 17:51:41 7.945u 0.174s 0:08.49 95.5% 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 Sun Oct 9 2011 at 17:51:41 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5232 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.470888 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): 3.278000 68.11300 ymin,ymax (A): -8.778000 53.34100 zmin,zma (A): -0.8030000 63.47700 x,y,z range (A): 64.83500 62.11900 64.28000 scale (grids/A): 2.470888 object centre (A): 35.69550 22.28150 31.33700 number of atom coordinates read : 5232 total number of charged atoms : 5085 net assigned charge : 1.635045 assigned positive charge : 806.7024 centred at (gu) : 81.49310 86.16139 85.64734 assigned negative charge : -805.0735 centred at (gu) : 80.82003 86.33238 85.44410 start vw surface at 0.2200000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 266124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41234 grid for indexing accessible points = 1.400000 m= 133054 mr = 201810 m= 41769 mr = 108150 m= 7568 mr = 32250 m= 643 mr = 5160 m= 13 mr = 315 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 101486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 40633 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) : 1.647258 object centre at (A) : 35.69550 22.28150 31.33700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5488871 -0.1960360 midg,1,midg; midg,igrid,midg 0.1602764 -1.8901156E-02 1,midg,midg; igrid,midg,midg -0.6121986 0.2018102 gauss-seidel spectral radius is 0.9992517 estimated iterations to convergence 289 setup time was (sec) 2.410000 now iterating at: 17:51:44 rms-change max change #iterations 12.29795 321.5172 at 10iterations 7.237701 138.8416 at 20iterations 4.232873 98.95972 at 30iterations 2.462151 43.63963 at 40iterations 1.429648 25.00384 at 50iterations 0.8269776 16.59854 at 60iterations 0.4780603 8.167895 at 70iterations 0.2754438 4.916916 at 80iterations 0.1587593 2.785294 at 90iterations 9.1675453E-02 1.570961 at 100iterations 5.2862938E-02 0.8102565 at 110iterations 3.0590652E-02 0.5675135 at 120iterations 1.7886046E-02 0.3205109 at 130iterations 1.0650935E-02 0.1813831 at 140iterations 6.5499339E-03 0.1202583 at 150iterations 4.2474996E-03 6.8563461E-02 at 160iterations 2.9608870E-03 4.8952103E-02 at 170iterations 2.2081542E-03 3.5160065E-02 at 180iterations finished qdiffx linear iterations at : 17:51:54 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 2.2081542E-03 3.5160065E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 17:51:55 13.392u 0.179s 0:13.85 97.9% 0+0k 0+0io 0pf+0w