Fri Dec 30 16:57:08 PST 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+sph.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 Fri Dec 30 2011 at 16:57:08 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 !!! WARNING: GLU 12 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5392224 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): -26.93800 26.60100 ymin,ymax (A): 8.518000 51.12100 zmin,zma (A): -11.84900 54.17200 x,y,z range (A): 53.53900 42.60300 66.02100 scale (grids/A): 0.5392224 object centre (A): -0.1684999 29.81950 21.16150 number of atom coordinates read : 2820 total number of charged atoms : 2704 net assigned charge : 2.000007 assigned positive charge : 420.4787 centred at (gu) : 91.18899 90.61964 90.34456 assigned negative charge : -418.4794 centred at (gu) : 91.20801 90.63401 90.32413 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5292 nv = 96 ne = 84 npr = 56209 no. pairs analyzed = 56209 no. exposed pairs = 3745 no. arc points = 26252 no. surface atoms = 1248 nbur = 1572 mkacc time = 0.1100000 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= 201 mr = 2572 m= 0 mr = 7 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2726 ## 359 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0364006E-12 2.1247057E-10 midg,1,midg; midg,igrid,midg 1.4223428E-10 3.0642079E-11 1,midg,midg; igrid,midg,midg 1.4028248E-10 3.9446692E-12 gauss-seidel spectral radius is 0.9822631 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 16:57:09 rms-change max change #iterations 6.4375833E-02 10.41094 at 10iterations 4.0813638E-03 0.7406940 at 20iterations 2.6045935E-04 4.1211128E-02 at 30iterations 1.6592536E-05 2.9973984E-03 at 40iterations 1.1267144E-06 2.0885468E-04 at 50iterations finished qdiffx linear iterations at : 16:57:12 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.1267144E-06 2.0885468E-04 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 16:57:12 3.562u 0.197s 0:04.09 91.6% 0+0k 1896+45912io 3pf+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 Fri Dec 30 2011 at 16:57:12 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 !!! WARNING: GLU 12 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.617667 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): -26.93800 26.60100 ymin,ymax (A): 8.518000 51.12100 zmin,zma (A): -11.84900 54.17200 x,y,z range (A): 53.53900 42.60300 66.02100 scale (grids/A): 1.617667 object centre (A): -0.1684999 29.81950 21.16150 number of atom coordinates read : 2820 total number of charged atoms : 2704 net assigned charge : 2.000007 assigned positive charge : 420.4787 centred at (gu) : 93.56671 91.85844 91.03311 assigned negative charge : -418.4794 centred at (gu) : 93.62379 91.90178 90.97195 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 58863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26252 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17070 mr = 38701 m= 1649 mr = 11073 m= 34 mr = 736 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 27106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 334 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20684 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) : 0.5392224 object centre at (A) : -0.1684999 29.81950 21.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8753786E-02 -2.1808802E-03 midg,1,midg; midg,igrid,midg -2.2448613E-03 4.7057257E-03 1,midg,midg; igrid,midg,midg 3.9289575E-03 1.1019659E-03 gauss-seidel spectral radius is 0.9981313 estimated iterations to convergence 184 setup time was (sec) 0.5700000 now iterating at: 16:57:13 rms-change max change #iterations 3.151376 184.3271 at 10iterations 1.294173 49.36185 at 20iterations 0.5330591 20.20713 at 30iterations 0.2209781 8.142595 at 40iterations 9.0906650E-02 3.455940 at 50iterations 3.7525289E-02 1.366294 at 60iterations 1.5465949E-02 0.5473518 at 70iterations 6.3651046E-03 0.2516482 at 80iterations 2.6238714E-03 0.1030402 at 90iterations 1.0821584E-03 4.0809631E-02 at 100iterations 4.4562054E-04 1.6506195E-02 at 110iterations 1.8470988E-04 6.6719055E-03 at 120iterations finished qdiffx linear iterations at : 16:57:20 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 1.8470988E-04 6.6719055E-03 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 16:57:21 7.934u 0.212s 0:08.70 93.5% 0+0k 0+45280io 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 Fri Dec 30 2011 at 16:57:21 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 !!! WARNING: GLU 12 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.426501 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): -26.93800 26.60100 ymin,ymax (A): 8.518000 51.12100 zmin,zma (A): -11.84900 54.17200 x,y,z range (A): 53.53900 42.60300 66.02100 scale (grids/A): 2.426501 object centre (A): -0.1684999 29.81950 21.16150 number of atom coordinates read : 2820 total number of charged atoms : 2704 net assigned charge : 2.000007 assigned positive charge : 420.4787 centred at (gu) : 95.34987 92.78747 91.54942 assigned negative charge : -418.4794 centred at (gu) : 95.43575 92.85271 91.45802 start vw surface at 0.1100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 136806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26252 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 59921 mr = 95451 m= 15967 mr = 45727 m= 2492 mr = 11469 m= 161 mr = 1524 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 61119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 21611 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) : 1.617667 object centre at (A) : -0.1684999 29.81950 21.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5256020 -0.2139138 midg,1,midg; midg,igrid,midg -5.2332852E-02 7.7850811E-02 1,midg,midg; igrid,midg,midg 7.4075356E-02 1.2743059E-02 gauss-seidel spectral radius is 0.9991204 estimated iterations to convergence 266 setup time was (sec) 1.130000 now iterating at: 16:57:22 rms-change max change #iterations 8.286449 346.8109 at 10iterations 4.657401 183.6637 at 20iterations 2.602675 61.30092 at 30iterations 1.443645 34.54309 at 40iterations 0.7980235 21.04954 at 50iterations 0.4394046 10.82090 at 60iterations 0.2419715 6.315004 at 70iterations 0.1324850 2.841069 at 80iterations 7.2585903E-02 1.671893 at 90iterations 3.9810903E-02 0.9170792 at 100iterations 2.1794988E-02 0.5049286 at 110iterations 1.1919527E-02 0.2491078 at 120iterations 6.5161348E-03 0.1364708 at 130iterations 3.5585584E-03 8.9549065E-02 at 140iterations 1.9436560E-03 4.5095444E-02 at 150iterations 1.0611129E-03 2.3237228E-02 at 160iterations 5.7970971E-04 1.2239218E-02 at 170iterations 3.1703405E-04 8.2126856E-03 at 180iterations finished qdiffx linear iterations at : 16:57:33 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 3.1703405E-04 8.2126856E-03 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 16:57:34 12.568u 0.207s 0:13.07 97.6% 0+0k 0+45272io 0pf+0w