Sat Oct 15 14:18:28 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 Sat Oct 15 2011 at 14:18:28 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5103943 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): -18.56900 36.74800 ymin,ymax (A): -30.70600 35.60500 zmin,zma (A): -4.241000 65.50900 x,y,z range (A): 55.31700 66.31100 69.75000 scale (grids/A): 0.5103943 object centre (A): 9.089500 2.449501 30.63400 number of atom coordinates read : 4846 total number of charged atoms : 4596 net assigned charge : 5.706026 assigned positive charge : 729.5582 centred at (gu) : 90.29286 90.36696 88.43221 assigned negative charge : -723.8569 centred at (gu) : 90.18784 90.36674 88.42847 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8029 nv = 96 ne = 84 npr = 97546 no. pairs analyzed = 97546 no. exposed pairs = 6281 no. arc points = 43176 no. surface atoms = 2104 nbur = 2742 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 = 1.680000 m= 281 mr = 4076 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4148 ## 609 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0419424E-10 5.9726606E-11 midg,1,midg; midg,igrid,midg 7.1754463E-11 8.7852184E-11 1,midg,midg; igrid,midg,midg -1.8233036E-10 3.7671713E-10 gauss-seidel spectral radius is 0.9803755 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 14:18:29 rms-change max change #iterations 6.8813287E-02 10.96046 at 10iterations 4.5205480E-03 0.7737236 at 20iterations 7.5356488E-04 0.1093826 at 30iterations 2.5944188E-04 3.0077219E-02 at 40iterations 1.0376798E-04 1.2691021E-02 at 50iterations finished qdiffx linear iterations at : 14:18:34 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.0376798E-04 1.2691021E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 14:18:34 3.650u 0.205s 0:05.98 64.3% 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 15 2011 at 14:18:34 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.531183 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): -18.56900 36.74800 ymin,ymax (A): -30.70600 35.60500 zmin,zma (A): -4.241000 65.50900 x,y,z range (A): 55.31700 66.31100 69.75000 scale (grids/A): 1.531183 object centre (A): 9.089500 2.449501 30.63400 number of atom coordinates read : 4846 total number of charged atoms : 4596 net assigned charge : 5.706026 assigned positive charge : 729.5582 centred at (gu) : 90.87750 91.09946 85.29517 assigned negative charge : -723.8569 centred at (gu) : 90.56312 91.10000 85.28497 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 90950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43176 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25704 mr = 62044 m= 2161 mr = 16551 m= 43 mr = 826 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 39437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 584 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 34503 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) : 0.5103943 object centre at (A) : 9.089500 2.449501 30.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7875896E-03 1.9495403E-02 midg,1,midg; midg,igrid,midg 1.9071852E-04 -6.6309157E-03 1,midg,midg; igrid,midg,midg -1.2855814E-03 1.2186061E-02 gauss-seidel spectral radius is 0.9981222 estimated iterations to convergence 183 setup time was (sec) 0.6700000 now iterating at: 14:18:36 rms-change max change #iterations 3.833427 168.0366 at 10iterations 1.569651 56.71228 at 20iterations 0.6459087 21.10729 at 30iterations 0.2666067 8.869225 at 40iterations 0.1094845 3.512590 at 50iterations 4.5303289E-02 1.362524 at 60iterations 1.8647423E-02 0.5638371 at 70iterations 7.7374801E-03 0.2751465 at 80iterations 3.2645871E-03 0.1172748 at 90iterations 1.4229915E-03 4.6989441E-02 at 100iterations 6.6799595E-04 2.1179199E-02 at 110iterations 3.6059928E-04 1.1746407E-02 at 120iterations finished qdiffx linear iterations at : 14:18:47 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 3.6059928E-04 1.1746407E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 14:18:47 8.285u 0.229s 0:12.75 66.6% 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 14:18:47 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.296774 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): -18.56900 36.74800 ymin,ymax (A): -30.70600 35.60500 zmin,zma (A): -4.241000 65.50900 x,y,z range (A): 55.31700 66.31100 69.75000 scale (grids/A): 2.296774 object centre (A): 9.089500 2.449501 30.63400 number of atom coordinates read : 4846 total number of charged atoms : 4596 net assigned charge : 5.706026 assigned positive charge : 729.5582 centred at (gu) : 91.31596 91.64909 82.94241 assigned negative charge : -723.8569 centred at (gu) : 90.84466 91.64993 82.92741 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 212392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43176 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93573 mr = 153231 m= 22365 mr = 72305 m= 2976 mr = 15453 m= 167 mr = 1709 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 88721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 36691 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) : 1.531183 object centre at (A) : 9.089500 2.449501 30.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1251549 0.4867735 midg,1,midg; midg,igrid,midg -0.1053375 -0.1976536 1,midg,midg; igrid,midg,midg -1.6517775E-02 0.1893350 gauss-seidel spectral radius is 0.9991704 estimated iterations to convergence 274 setup time was (sec) 1.350000 now iterating at: 14:18:49 rms-change max change #iterations 10.43923 275.9328 at 10iterations 6.025755 156.9024 at 20iterations 3.450597 78.65723 at 30iterations 1.965302 42.99552 at 40iterations 1.113389 25.10490 at 50iterations 0.6288307 13.96810 at 60iterations 0.3533205 6.972655 at 70iterations 0.1983572 4.191658 at 80iterations 0.1113758 2.547144 at 90iterations 6.2233597E-02 1.344291 at 100iterations 3.4838952E-02 0.6591110 at 110iterations 1.9495858E-02 0.3574476 at 120iterations 1.0881620E-02 0.2082977 at 130iterations 6.0678548E-03 0.1149349 at 140iterations 3.3963139E-03 7.0782661E-02 at 150iterations 1.8963207E-03 3.7923813E-02 at 160iterations 1.0702135E-03 2.0511627E-02 at 170iterations 6.0508365E-04 1.1578321E-02 at 180iterations finished qdiffx linear iterations at : 14:19:02 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 6.0508365E-04 1.1578321E-02 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 14:19:03 14.021u 0.255s 0:15.77 90.4% 0+0k 0+0io 0pf+0w