Wed Feb 15 08:56:31 PST 2012 #!/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+sph_thinner.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 = amb.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 Wed Feb 15 2012 at 08:56:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 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: 0.6135815 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 0.6135815 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.500033 assigned positive charge : 399.6616 centred at (gu) : 90.14949 93.14500 89.01158 assigned negative charge : -390.1628 centred at (gu) : 90.18662 93.20668 89.04218 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6780 nv = 96 ne = 84 npr = 53600 no. pairs analyzed = 53600 no. exposed pairs = 3877 no. arc points = 27387 no. surface atoms = 1300 nbur = 1400 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 3256 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2725 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8878008E-09 3.7585601E-09 midg,1,midg; midg,igrid,midg 4.9068363E-09 5.5299463E-09 1,midg,midg; igrid,midg,midg 8.0537674E-09 4.3994599E-09 gauss-seidel spectral radius is 0.9862673 estimated iterations to convergence 70 setup time was (sec) 0.5700000 now iterating at: 08:56:32 rms-change max change #iterations 0.1175918 17.74361 at 10iterations 1.0771351E-02 1.731621 at 20iterations 1.0341494E-03 0.1464691 at 30iterations 1.3592203E-04 1.9309998E-02 at 40iterations 2.8327268E-05 4.3926239E-03 at 50iterations finished qdiffx linear iterations at : 08:56:35 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.8327268E-05 4.3926239E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 08:56:36 3.612u 0.172s 0:04.21 89.7% 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 Wed Feb 15 2012 at 08:56:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 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: 1.840744 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 1.840744 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.500033 assigned positive charge : 399.6616 centred at (gu) : 90.44785 99.43443 87.03401 assigned negative charge : -390.1628 centred at (gu) : 90.55984 99.62000 87.12672 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27387 grid for indexing accessible points = 1.400000 m= 25290 mr = 46352 m= 4328 mr = 17415 m= 282 mr = 2520 m= 5 mr = 87 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 0.5900000 number of dielectric boundary points 36243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20063 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) : 0.6135815 object centre at (A) : 13.67150 -6.216001 32.62950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8813762E-03 1.2185872E-02 midg,1,midg; midg,igrid,midg 3.2855798E-02 5.3040355E-02 1,midg,midg; igrid,midg,midg 1.6864091E-02 2.5999593E-02 gauss-seidel spectral radius is 0.9985648 estimated iterations to convergence 209 setup time was (sec) 0.9000000 now iterating at: 08:56:38 rms-change max change #iterations 3.990194 172.0240 at 10iterations 1.837866 70.21768 at 20iterations 0.8460919 28.90426 at 30iterations 0.3872602 13.28077 at 40iterations 0.1783743 5.906712 at 50iterations 8.1958987E-02 2.848927 at 60iterations 3.7723113E-02 1.168892 at 70iterations 1.7320056E-02 0.5936680 at 80iterations 7.9797078E-03 0.2657967 at 90iterations 3.6778923E-03 0.1285028 at 100iterations 1.6942160E-03 5.4374695E-02 at 110iterations 7.8582304E-04 2.9286861E-02 at 120iterations finished qdiffx linear iterations at : 08:56:46 total time elapsed so far: 8.550000 # loops : 120 mean,max change (kT/e) : 7.8582304E-04 2.9286861E-02 energy calculations done at 8.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.750000 DelPhi exited at 08:56:47 8.754u 0.275s 0:10.54 85.5% 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 Wed Feb 15 2012 at 08:56:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 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: 2.761117 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 2.761117 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.500033 assigned positive charge : 399.6616 centred at (gu) : 90.67141 104.1513 85.55090 assigned negative charge : -390.1628 centred at (gu) : 90.83968 104.4300 85.68992 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 167839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27387 grid for indexing accessible points = 1.400000 m= 80539 mr = 113920 m= 30176 mr = 62417 m= 7582 mr = 23176 m= 1075 mr = 5463 m= 69 mr = 651 m= 0 mr = 9 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.500000 number of dielectric boundary points 81644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 20502 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) : 1.840744 object centre at (A) : 13.67150 -6.216001 32.62950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9700965E-03 0.1433212 midg,1,midg; midg,igrid,midg 0.3586750 0.9038032 1,midg,midg; igrid,midg,midg 0.1425339 0.3814029 gauss-seidel spectral radius is 0.9992635 estimated iterations to convergence 291 setup time was (sec) 1.840000 now iterating at: 08:56:49 rms-change max change #iterations 9.885224 342.9550 at 10iterations 5.906422 143.7039 at 20iterations 3.494115 73.24118 at 30iterations 2.050347 40.81601 at 40iterations 1.196898 23.74890 at 50iterations 0.6967539 13.07471 at 60iterations 0.4058555 8.519552 at 70iterations 0.2351629 4.997681 at 80iterations 0.1361706 2.782626 at 90iterations 7.8628637E-02 1.441544 at 100iterations 4.5423176E-02 0.8145504 at 110iterations 2.6181091E-02 0.4853911 at 120iterations 1.5098905E-02 0.2957840 at 130iterations 8.7280786E-03 0.1602130 at 140iterations 5.0455611E-03 0.1047692 at 150iterations 2.9178266E-03 6.1608791E-02 at 160iterations 1.6936391E-03 3.3357620E-02 at 170iterations 9.9041231E-04 2.0387650E-02 at 180iterations finished qdiffx linear iterations at : 08:57:01 total time elapsed so far: 14.05000 # loops : 180 mean,max change (kT/e) : 9.9041231E-04 2.0387650E-02 energy calculations done at 14.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.24000 DelPhi exited at 08:57:01 14.244u 0.271s 0:14.81 97.9% 0+0k 0+0io 0pf+0w