Sat Oct 15 14:27:26 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 14:27:26 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2953 !!! WARNING: HIR 148 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5465823 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): -2.029000 63.10300 ymin,ymax (A): 11.88600 58.87400 zmin,zma (A): -7.750000 39.86800 x,y,z range (A): 65.13200 46.98800 47.61800 scale (grids/A): 0.5465823 object centre (A): 30.53700 35.38000 16.05900 number of atom coordinates read : 2953 total number of charged atoms : 2812 net assigned charge : -4.485960 assigned positive charge : 441.6430 centred at (gu) : 89.61016 89.68533 89.51689 assigned negative charge : -446.1301 centred at (gu) : 89.53306 89.83934 89.46911 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5660 nv = 96 ne = 84 npr = 59369 no. pairs analyzed = 59369 no. exposed pairs = 3840 no. arc points = 27160 no. surface atoms = 1307 nbur = 1646 mkacc time = 0.1000000 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 = 1.596000 m= 235 mr = 2825 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2764 ## 363 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7454 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9011297E-10 3.3616804E-11 midg,1,midg; midg,igrid,midg 8.0882973E-10 -1.2538222E-09 1,midg,midg; igrid,midg,midg -8.9858992E-10 2.1326210E-10 gauss-seidel spectral radius is 0.9827434 estimated iterations to convergence 63 setup time was (sec) 0.4200000 now iterating at: 14:27:27 rms-change max change #iterations 7.2255626E-02 14.54576 at 10iterations 4.8453547E-03 0.8824444 at 20iterations 3.2115707E-04 5.5011749E-02 at 30iterations 2.1861739E-05 3.3798218E-03 at 40iterations 1.4720250E-06 2.5558472E-04 at 50iterations finished qdiffx linear iterations at : 14:27:31 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.4720250E-06 2.5558472E-04 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 14:27:32 3.598u 0.205s 0:05.46 69.4% 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 14:27:32 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2953 !!! WARNING: HIR 148 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.639747 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): -2.029000 63.10300 ymin,ymax (A): 11.88600 58.87400 zmin,zma (A): -7.750000 39.86800 x,y,z range (A): 65.13200 46.98800 47.61800 scale (grids/A): 1.639747 object centre (A): 30.53700 35.38000 16.05900 number of atom coordinates read : 2953 total number of charged atoms : 2812 net assigned charge : -4.485960 assigned positive charge : 441.6430 centred at (gu) : 88.82969 89.05500 88.55022 assigned negative charge : -446.1301 centred at (gu) : 88.59905 89.51799 88.40704 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27160 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18709 mr = 41332 m= 1721 mr = 12687 m= 30 mr = 716 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 508 time to turn everything in is 0.3100000 number of dielectric boundary points 28480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 289 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 21555 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) : 0.5465823 object centre at (A) : 30.53700 35.38000 16.05900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8865712E-03 -1.5447855E-03 midg,1,midg; midg,igrid,midg 8.7695261E-03 -1.6415861E-02 1,midg,midg; igrid,midg,midg -2.2839677E-02 9.2466101E-03 gauss-seidel spectral radius is 0.9981992 estimated iterations to convergence 187 setup time was (sec) 0.5500000 now iterating at: 14:27:33 rms-change max change #iterations 3.362446 169.0958 at 10iterations 1.397512 52.43457 at 20iterations 0.5830830 21.55856 at 30iterations 0.2446701 9.268852 at 40iterations 0.1022941 3.847157 at 50iterations 4.2677399E-02 1.643288 at 60iterations 1.7738152E-02 0.6754971 at 70iterations 7.4297250E-03 0.2770042 at 80iterations 3.1137548E-03 0.1151161 at 90iterations 1.3024381E-03 4.7319412E-02 at 100iterations 5.4522720E-04 1.8638611E-02 at 110iterations 2.2790741E-04 8.7471008E-03 at 120iterations finished qdiffx linear iterations at : 14:27:47 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 2.2790741E-04 8.7471008E-03 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 14:27:47 8.065u 0.224s 0:15.55 53.2% 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 14:27:47 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2953 !!! WARNING: HIR 148 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.459620 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): -2.029000 63.10300 ymin,ymax (A): 11.88600 58.87400 zmin,zma (A): -7.750000 39.86800 x,y,z range (A): 65.13200 46.98800 47.61800 scale (grids/A): 2.459620 object centre (A): 30.53700 35.38000 16.05900 number of atom coordinates read : 2953 total number of charged atoms : 2812 net assigned charge : -4.485960 assigned positive charge : 441.6430 centred at (gu) : 88.24443 88.58241 87.82488 assigned negative charge : -446.1301 centred at (gu) : 87.89839 89.27686 87.61036 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 145586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27160 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 65235 mr = 101553 m= 18132 mr = 50818 m= 2624 mr = 13394 m= 136 mr = 1605 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1753 time to turn everything in is 0.7600000 number of dielectric boundary points 64302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22478 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) : 1.639747 object centre at (A) : 30.53700 35.38000 16.05900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4006012E-02 -2.7214654E-02 midg,1,midg; midg,igrid,midg 0.1493494 -0.2228400 1,midg,midg; igrid,midg,midg -0.5456426 0.5070973 gauss-seidel spectral radius is 0.9991467 estimated iterations to convergence 270 setup time was (sec) 1.010000 now iterating at: 14:27:49 rms-change max change #iterations 8.696308 325.2653 at 10iterations 4.880731 125.1201 at 20iterations 2.729168 81.21678 at 30iterations 1.519224 39.48569 at 40iterations 0.8424502 18.68521 at 50iterations 0.4673200 10.98429 at 60iterations 0.2581788 5.308899 at 70iterations 0.1424484 2.978683 at 80iterations 7.8635141E-02 1.733215 at 90iterations 4.3440055E-02 0.9548182 at 100iterations 2.3933664E-02 0.5167940 at 110iterations 1.3211004E-02 0.2722168 at 120iterations 7.2726109E-03 0.1570139 at 130iterations 4.0076082E-03 0.1010284 at 140iterations 2.2086906E-03 4.3563843E-02 at 150iterations 1.2135092E-03 2.4469852E-02 at 160iterations 6.7037885E-04 1.4002337E-02 at 170iterations 3.6964857E-04 7.3814392E-03 at 180iterations finished qdiffx linear iterations at : 14:28:01 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 3.6964857E-04 7.3814392E-03 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 14:28:01 12.946u 0.249s 0:13.89 94.8% 0+0k 0+0io 0pf+0w