Mon Oct 10 19:34:41 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 Mon Oct 10 2011 at 19:34:41 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 !!! WARNING: HIR 239 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6253183 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): -37.43500 18.99300 ymin,ymax (A): -36.88800 20.04300 zmin,zma (A): -27.59000 24.81000 x,y,z range (A): 56.42800 56.93100 52.40000 scale (grids/A): 0.6253183 object centre (A): -9.220999 -8.422501 -1.390000 number of atom coordinates read : 2946 total number of charged atoms : 2804 net assigned charge : 3.014013 assigned positive charge : 444.0374 centred at (gu) : 87.31676 90.40406 89.45924 assigned negative charge : -441.0247 centred at (gu) : 87.25282 90.54003 89.46256 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7939 nv = 96 ne = 84 npr = 56145 no. pairs analyzed = 56145 no. exposed pairs = 4206 no. arc points = 30547 no. surface atoms = 1410 nbur = 1536 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 446 mr = 3760 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3001 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7561754E-09 2.4693965E-09 midg,1,midg; midg,igrid,midg 1.3484144E-08 -9.8470299E-09 1,midg,midg; igrid,midg,midg -4.8725166E-09 4.8223865E-09 gauss-seidel spectral radius is 0.9868077 estimated iterations to convergence 71 setup time was (sec) 0.7900000 now iterating at: 19:34:42 rms-change max change #iterations 0.1416961 21.36006 at 10iterations 1.3157374E-02 2.075375 at 20iterations 1.2644361E-03 0.1967931 at 30iterations 1.4103029E-04 2.0946503E-02 at 40iterations 3.0043115E-05 4.3203831E-03 at 50iterations finished qdiffx linear iterations at : 19:34:46 total time elapsed so far: 4.720000 # loops : 50 mean,max change (kT/e) : 3.0043115E-05 4.3203831E-03 energy calculations done at 4.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.950000 DelPhi exited at 19:34:46 4.951u 0.387s 0:05.65 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 Mon Oct 10 2011 at 19:34:46 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 !!! WARNING: HIR 239 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.875955 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): -37.43500 18.99300 ymin,ymax (A): -36.88800 20.04300 zmin,zma (A): -27.59000 24.81000 x,y,z range (A): 56.42800 56.93100 52.40000 scale (grids/A): 1.875955 object centre (A): -9.220999 -8.422501 -1.390000 number of atom coordinates read : 2946 total number of charged atoms : 2804 net assigned charge : 3.014013 assigned positive charge : 444.0374 centred at (gu) : 81.94955 91.21155 88.37676 assigned negative charge : -441.0247 centred at (gu) : 81.75848 91.61985 88.38771 start vw surface at 0.1600000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 83776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30547 grid for indexing accessible points = 1.400000 m= 28468 mr = 52741 m= 4917 mr = 19394 m= 270 mr = 2679 m= 7 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 42575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 22032 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) : 0.6253183 object centre at (A) : -9.220999 -8.422501 -1.390000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9944938E-02 2.3073297E-02 midg,1,midg; midg,igrid,midg 2.5488887E-02 -6.0326778E-03 1,midg,midg; igrid,midg,midg -3.1075724E-03 5.8748284E-03 gauss-seidel spectral radius is 0.9986632 estimated iterations to convergence 217 setup time was (sec) 1.200000 now iterating at: 19:34:48 rms-change max change #iterations 4.504904 171.7028 at 10iterations 2.113336 71.36433 at 20iterations 0.9951589 34.38787 at 30iterations 0.4683461 16.31075 at 40iterations 0.2202663 6.383566 at 50iterations 0.1039966 3.211484 at 60iterations 4.8813380E-02 1.542336 at 70iterations 2.3005046E-02 0.6818285 at 80iterations 1.0849237E-02 0.3785722 at 90iterations 5.1304880E-03 0.1679192 at 100iterations 2.4217444E-03 7.8173637E-02 at 110iterations 1.1527643E-03 3.3977509E-02 at 120iterations finished qdiffx linear iterations at : 19:34:58 total time elapsed so far: 11.43000 # loops : 120 mean,max change (kT/e) : 1.1527643E-03 3.3977509E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.64000 DelPhi exited at 19:34:59 11.644u 0.487s 0:12.80 94.6% 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 Mon Oct 10 2011 at 19:34:59 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 !!! WARNING: HIR 239 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.813933 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): -37.43500 18.99300 ymin,ymax (A): -36.88800 20.04300 zmin,zma (A): -27.59000 24.81000 x,y,z range (A): 56.42800 56.93100 52.40000 scale (grids/A): 2.813933 object centre (A): -9.220999 -8.422501 -1.390000 number of atom coordinates read : 2946 total number of charged atoms : 2804 net assigned charge : 3.014013 assigned positive charge : 444.0374 centred at (gu) : 77.92416 91.81720 87.56487 assigned negative charge : -441.0247 centred at (gu) : 77.63753 92.42983 87.58152 start vw surface at 0.1500000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 193185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30547 grid for indexing accessible points = 1.400000 m= 90536 mr = 129451 m= 33948 mr = 69588 m= 8597 mr = 25865 m= 1075 mr = 5889 m= 49 mr = 542 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.410000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.280000 number of dielectric boundary points 96048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.440000 number of grid points assigned charge 22426 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) : 1.875955 object centre at (A) : -9.220999 -8.422501 -1.390000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2968491 0.3852232 midg,1,midg; midg,igrid,midg 0.4951524 -4.4880990E-02 1,midg,midg; igrid,midg,midg -0.2290814 9.4925530E-02 gauss-seidel spectral radius is 0.9993113 estimated iterations to convergence 301 setup time was (sec) 2.650000 now iterating at: 19:35:03 rms-change max change #iterations 10.94684 358.6817 at 10iterations 6.667517 146.9020 at 20iterations 3.995798 86.46228 at 30iterations 2.395258 48.70110 at 40iterations 1.427294 30.17667 at 50iterations 0.8473192 15.54577 at 60iterations 0.5020558 8.443910 at 70iterations 0.2969313 5.160355 at 80iterations 0.1748468 2.957355 at 90iterations 0.1031522 1.910442 at 100iterations 6.0726244E-02 1.015579 at 110iterations 3.5713375E-02 0.6694078 at 120iterations 2.0988187E-02 0.3689995 at 130iterations 1.2319580E-02 0.2195787 at 140iterations 7.2356584E-03 0.1241322 at 150iterations 4.2460496E-03 7.0607185E-02 at 160iterations 2.4961508E-03 4.2490005E-02 at 170iterations 1.4724126E-03 2.4538040E-02 at 180iterations finished qdiffx linear iterations at : 19:35:20 total time elapsed so far: 20.34000 # loops : 180 mean,max change (kT/e) : 1.4724126E-03 2.4538040E-02 energy calculations done at 20.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.56000 DelPhi exited at 19:35:21 20.566u 0.518s 0:21.41 98.4% 0+0k 0+0io 0pf+0w