Mon Oct 10 17:03:33 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 17:03:33 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 = 4816 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5134344 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): -18.64900 37.36900 ymin,ymax (A): -30.70500 34.33400 zmin,zma (A): -3.939000 65.39800 x,y,z range (A): 56.01801 65.03900 69.33701 scale (grids/A): 0.5134344 object centre (A): 9.360002 1.814500 30.72950 number of atom coordinates read : 4816 total number of charged atoms : 4566 net assigned charge : 8.706045 assigned positive charge : 723.4896 centred at (gu) : 90.13976 90.52916 88.42365 assigned negative charge : -714.7878 centred at (gu) : 90.03658 90.59674 88.39283 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8097 nv = 96 ne = 84 npr = 96628 no. pairs analyzed = 96628 no. exposed pairs = 6196 no. arc points = 42761 no. surface atoms = 2073 nbur = 2743 mkacc time = 0.2100000 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 = 1.652000 m= 308 mr = 4165 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4073 ## 549 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10664 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5254233E-11 1.5462001E-10 midg,1,midg; midg,igrid,midg 2.9423372E-10 -6.6554456E-11 1,midg,midg; igrid,midg,midg -1.5703076E-10 4.5575088E-10 gauss-seidel spectral radius is 0.9806061 estimated iterations to convergence 59 setup time was (sec) 0.6600000 now iterating at: 17:03:33 rms-change max change #iterations 7.1766809E-02 10.72162 at 10iterations 4.2467769E-03 0.6245241 at 20iterations 4.4977482E-04 5.8357716E-02 at 30iterations 1.3946729E-04 2.0483971E-02 at 40iterations 5.5022516E-05 9.0804100E-03 at 50iterations finished qdiffx linear iterations at : 17:03:36 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 5.5022516E-05 9.0804100E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 17:03:37 3.261u 0.142s 0:04.65 73.1% 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 17:03:37 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 = 4816 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.540303 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): -18.64900 37.36900 ymin,ymax (A): -30.70500 34.33400 zmin,zma (A): -3.939000 65.39800 x,y,z range (A): 56.01801 65.03900 69.33701 scale (grids/A): 1.540303 object centre (A): 9.360002 1.814500 30.72950 number of atom coordinates read : 4816 total number of charged atoms : 4566 net assigned charge : 8.706045 assigned positive charge : 723.4896 centred at (gu) : 90.41813 91.58623 85.26933 assigned negative charge : -714.7878 centred at (gu) : 90.10974 91.79003 85.17819 start vw surface at 0.2500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 91934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42761 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26500 mr = 62902 m= 2300 mr = 17432 m= 40 mr = 881 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 110 time to turn everything in is 0.7000000 number of dielectric boundary points 39557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 588 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 34344 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) : 0.5134344 object centre at (A) : 9.360002 1.814500 30.72950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3502757E-03 2.1466032E-02 midg,1,midg; midg,igrid,midg 1.2499960E-02 -1.2033148E-02 1,midg,midg; igrid,midg,midg -1.7890208E-04 1.3187393E-02 gauss-seidel spectral radius is 0.9981447 estimated iterations to convergence 184 setup time was (sec) 0.9500000 now iterating at: 17:03:38 rms-change max change #iterations 3.862137 209.2794 at 10iterations 1.596101 54.74478 at 20iterations 0.6613793 22.79745 at 30iterations 0.2725230 9.602381 at 40iterations 0.1125660 3.786501 at 50iterations 4.6655100E-02 1.673019 at 60iterations 1.9309551E-02 0.5923004 at 70iterations 8.0041178E-03 0.2694225 at 80iterations 3.3300212E-03 0.1182184 at 90iterations 1.3936488E-03 4.4755936E-02 at 100iterations 5.9316232E-04 1.8314362E-02 at 110iterations 2.6500382E-04 8.6727142E-03 at 120iterations finished qdiffx linear iterations at : 17:03:44 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 2.6500382E-04 8.6727142E-03 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 17:03:46 7.148u 0.186s 0:08.71 84.0% 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 17:03:46 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4816 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.310455 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): -18.64900 37.36900 ymin,ymax (A): -30.70500 34.33400 zmin,zma (A): -3.939000 65.39800 x,y,z range (A): 56.01801 65.03900 69.33701 scale (grids/A): 2.310455 object centre (A): 9.360002 1.814500 30.72950 number of atom coordinates read : 4816 total number of charged atoms : 4566 net assigned charge : 8.706045 assigned positive charge : 723.4896 centred at (gu) : 90.62679 92.37904 82.90372 assigned negative charge : -714.7878 centred at (gu) : 90.16454 92.68508 82.76717 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 214263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42761 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95235 mr = 154971 m= 23984 mr = 73785 m= 3233 mr = 16949 m= 168 mr = 1829 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 308 time to turn everything in is 1.510000 number of dielectric boundary points 89288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 36394 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) : 1.540303 object centre at (A) : 9.360002 1.814500 30.72950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1596192 0.5073555 midg,1,midg; midg,igrid,midg 0.2622527 -0.3210315 1,midg,midg; igrid,midg,midg -1.9151871E-03 0.1940228 gauss-seidel spectral radius is 0.9991750 estimated iterations to convergence 275 setup time was (sec) 1.800000 now iterating at: 17:03:48 rms-change max change #iterations 10.42813 265.6949 at 10iterations 5.997334 140.7783 at 20iterations 3.422283 76.52451 at 30iterations 1.939794 38.34349 at 40iterations 1.098264 21.71626 at 50iterations 0.6185615 13.65781 at 60iterations 0.3480660 7.001916 at 70iterations 0.1954172 3.669574 at 80iterations 0.1095043 2.237460 at 90iterations 6.1451919E-02 1.257751 at 100iterations 3.4363464E-02 0.6267543 at 110iterations 1.9205805E-02 0.3924017 at 120iterations 1.0745560E-02 0.2056971 at 130iterations 5.9894528E-03 0.1140692 at 140iterations 3.3520025E-03 6.5996170E-02 at 150iterations 1.8719501E-03 3.4887314E-02 at 160iterations 1.0519378E-03 2.0381927E-02 at 170iterations 5.9268996E-04 1.1425972E-02 at 180iterations finished qdiffx linear iterations at : 17:03:58 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 5.9268996E-04 1.1425972E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.53000 DelPhi exited at 17:04:00 11.534u 0.180s 0:13.58 86.2% 0+0k 0+0io 0pf+0w