Sat Oct 15 15:13:40 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 15:13:40 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2879 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.6372277 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): -28.58500 27.02000 ymin,ymax (A): -3.658000 52.20900 zmin,zma (A): -0.7810000 52.96600 x,y,z range (A): 55.60500 55.86700 53.74700 scale (grids/A): 0.6372277 object centre (A): -0.7824993 24.27550 26.09250 number of atom coordinates read : 2879 total number of charged atoms : 2719 net assigned charge : 3.451021 assigned positive charge : 442.6295 centred at (gu) : 91.30168 91.09401 90.16642 assigned negative charge : -439.1790 centred at (gu) : 91.50407 91.01234 90.32729 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7807 nv = 96 ne = 84 npr = 57948 no. pairs analyzed = 57948 no. exposed pairs = 3531 no. arc points = 24492 no. surface atoms = 1190 nbur = 1689 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4405 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2440 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3367988E-08 -1.5585982E-08 midg,1,midg; midg,igrid,midg -3.9702228E-09 1.8787359E-08 1,midg,midg; igrid,midg,midg 2.1980506E-08 -2.7154632E-08 gauss-seidel spectral radius is 0.9872648 estimated iterations to convergence 72 setup time was (sec) 0.4300000 now iterating at: 15:13:41 rms-change max change #iterations 0.1583305 25.29934 at 10iterations 1.6191686E-02 2.311023 at 20iterations 1.8161149E-03 0.2624397 at 30iterations 3.0567250E-04 3.8261414E-02 at 40iterations 7.4224459E-05 9.0675354E-03 at 50iterations finished qdiffx linear iterations at : 15:13:44 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 7.4224459E-05 9.0675354E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 15:13:44 3.545u 0.177s 0:03.99 92.9% 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 15:13:44 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2879 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 1.911683 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): -28.58500 27.02000 ymin,ymax (A): -3.658000 52.20900 zmin,zma (A): -0.7810000 52.96600 x,y,z range (A): 55.60500 55.86700 53.74700 scale (grids/A): 1.911683 object centre (A): -0.7824993 24.27550 26.09250 number of atom coordinates read : 2879 total number of charged atoms : 2719 net assigned charge : 3.451021 assigned positive charge : 442.6295 centred at (gu) : 93.90448 93.28148 90.49873 assigned negative charge : -439.1790 centred at (gu) : 94.51174 93.03674 90.98165 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24492 grid for indexing accessible points = 1.400000 m= 31450 mr = 59173 m= 4891 mr = 23530 m= 304 mr = 3089 m= 5 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 737 time to turn everything in is 0.4200000 number of dielectric boundary points 35023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 21399 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) : 0.6372277 object centre at (A) : -0.7824993 24.27550 26.09250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7555130E-02 -1.1767472E-02 midg,1,midg; midg,igrid,midg 4.8682876E-03 6.5877992E-03 1,midg,midg; igrid,midg,midg 7.2919890E-02 -5.2669074E-02 gauss-seidel spectral radius is 0.9986740 estimated iterations to convergence 218 setup time was (sec) 0.6500000 now iterating at: 15:13:45 rms-change max change #iterations 4.631026 187.8505 at 10iterations 2.195810 81.06238 at 20iterations 1.039649 36.65906 at 30iterations 0.4928380 14.64233 at 40iterations 0.2335397 7.608999 at 50iterations 0.1112130 3.315887 at 60iterations 5.2677635E-02 1.588184 at 70iterations 2.5033873E-02 0.7572932 at 80iterations 1.1892735E-02 0.3610992 at 90iterations 5.6836605E-03 0.1775322 at 100iterations 2.7240783E-03 9.0956688E-02 at 110iterations 1.3216971E-03 3.7418365E-02 at 120iterations finished qdiffx linear iterations at : 15:13:53 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 1.3216971E-03 3.7418365E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 15:13:53 8.202u 0.233s 0:08.71 96.7% 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 15:13:53 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2879 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.867525 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): -28.58500 27.02000 ymin,ymax (A): -3.658000 52.20900 zmin,zma (A): -0.7810000 52.96600 x,y,z range (A): 55.60500 55.86700 53.74700 scale (grids/A): 2.867525 object centre (A): -0.7824993 24.27550 26.09250 number of atom coordinates read : 2879 total number of charged atoms : 2719 net assigned charge : 3.451021 assigned positive charge : 442.6295 centred at (gu) : 95.85660 94.92198 90.74797 assigned negative charge : -439.1790 centred at (gu) : 96.76759 94.55503 91.47233 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 194446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24492 grid for indexing accessible points = 1.400000 m= 100869 mr = 142543 m= 36870 mr = 83511 m= 8828 mr = 29894 m= 1308 mr = 6634 m= 80 mr = 861 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 2576 time to turn everything in is 1.090000 number of dielectric boundary points 78924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 21752 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) : 1.911683 object centre at (A) : -0.7824993 24.27550 26.09250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3331605 -0.1563173 midg,1,midg; midg,igrid,midg 0.1687278 -6.9359437E-02 1,midg,midg; igrid,midg,midg 0.7135429 -0.5920987 gauss-seidel spectral radius is 0.9992716 estimated iterations to convergence 292 setup time was (sec) 1.350000 now iterating at: 15:13:55 rms-change max change #iterations 10.82768 462.0424 at 10iterations 6.335218 125.4508 at 20iterations 3.696072 68.23646 at 30iterations 2.150013 40.27467 at 40iterations 1.247877 21.73326 at 50iterations 0.7242089 13.01986 at 60iterations 0.4202967 7.375925 at 70iterations 0.2429399 4.468716 at 80iterations 0.1407344 2.404264 at 90iterations 8.1419639E-02 1.393877 at 100iterations 4.7125947E-02 0.8873177 at 110iterations 2.7360935E-02 0.5507813 at 120iterations 1.5855391E-02 0.2804527 at 130iterations 9.2473170E-03 0.1565475 at 140iterations 5.4107565E-03 9.6719742E-02 at 150iterations 3.1961317E-03 6.2259674E-02 at 160iterations 1.9220115E-03 3.8215637E-02 at 170iterations 1.1879567E-03 2.3307800E-02 at 180iterations finished qdiffx linear iterations at : 15:14:07 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 1.1879567E-03 2.3307800E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 15:14:07 13.533u 0.255s 0:14.08 97.8% 0+0k 0+0io 0pf+0w