Sat Oct 15 14:12:04 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 14:12:05 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5223 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5057250 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): -18.80700 36.74700 ymin,ymax (A): -30.50600 32.38900 zmin,zma (A): -4.013000 66.38100 x,y,z range (A): 55.55400 62.89500 70.39400 scale (grids/A): 0.5057250 object centre (A): 8.970001 0.9414997 31.18400 number of atom coordinates read : 5223 total number of charged atoms : 4967 net assigned charge : 7.706048 assigned positive charge : 787.4264 centred at (gu) : 90.56529 90.70630 89.41160 assigned negative charge : -779.7256 centred at (gu) : 90.48339 90.73712 89.39021 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8299 nv = 96 ne = 84 npr = 106205 no. pairs analyzed = 106205 no. exposed pairs = 6375 no. arc points = 43844 no. surface atoms = 2176 nbur = 3047 mkacc time = 0.1900000 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 = 1.680000 m= 285 mr = 4333 m= 0 mr = 3 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4317 ## 684 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4192341E-11 1.1693480E-10 midg,1,midg; midg,igrid,midg 1.3116969E-10 1.9088085E-11 1,midg,midg; igrid,midg,midg -8.7487094E-11 3.1780820E-10 gauss-seidel spectral radius is 0.9800332 estimated iterations to convergence 59 setup time was (sec) 0.5900000 now iterating at: 14:12:07 rms-change max change #iterations 6.9374017E-02 9.882553 at 10iterations 4.5711221E-03 0.6179733 at 20iterations 8.7165902E-04 0.1102371 at 30iterations 3.1113270E-04 3.6205292E-02 at 40iterations 1.1844501E-04 1.3763428E-02 at 50iterations finished qdiffx linear iterations at : 14:12:14 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.1844501E-04 1.3763428E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 14:12:15 4.127u 0.279s 0:09.74 45.0% 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 Sat Oct 15 2011 at 14:12:15 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5223 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.517175 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): -18.80700 36.74700 ymin,ymax (A): -30.50600 32.38900 zmin,zma (A): -4.013000 66.38100 x,y,z range (A): 55.55400 62.89500 70.39400 scale (grids/A): 1.517175 object centre (A): 8.970001 0.9414997 31.18400 number of atom coordinates read : 5223 total number of charged atoms : 4967 net assigned charge : 7.706048 assigned positive charge : 787.4264 centred at (gu) : 91.69418 92.11737 88.23327 assigned negative charge : -779.7256 centred at (gu) : 91.45010 92.21141 88.17005 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 95507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43844 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27291 mr = 66430 m= 2325 mr = 18037 m= 61 mr = 986 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 39728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 612 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 37183 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) : 0.5057250 object centre at (A) : 8.970001 0.9414997 31.18400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1652699E-03 2.1151550E-02 midg,1,midg; midg,igrid,midg -4.3456606E-04 -1.2660458E-02 1,midg,midg; igrid,midg,midg -1.0623964E-03 1.1344657E-02 gauss-seidel spectral radius is 0.9981066 estimated iterations to convergence 183 setup time was (sec) 0.7300000 now iterating at: 14:12:16 rms-change max change #iterations 3.908908 160.4867 at 10iterations 1.597129 62.86114 at 20iterations 0.6553727 21.64755 at 30iterations 0.2688845 9.690405 at 40iterations 0.1098826 3.455059 at 50iterations 4.5229882E-02 1.427258 at 60iterations 1.8616106E-02 0.6267281 at 70iterations 7.7054850E-03 0.2314148 at 80iterations 3.2390291E-03 0.1021538 at 90iterations 1.4224672E-03 4.5189336E-02 at 100iterations 6.8304106E-04 2.2937775E-02 at 110iterations 3.7310357E-04 1.2416840E-02 at 120iterations finished qdiffx linear iterations at : 14:12:32 total time elapsed so far: 8.900000 # loops : 120 mean,max change (kT/e) : 3.7310357E-04 1.2416840E-02 energy calculations done at 8.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.030000 DelPhi exited at 14:12:33 9.030u 0.275s 0:18.10 51.3% 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 Sat Oct 15 2011 at 14:12:33 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5223 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.275762 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): -18.80700 36.74700 ymin,ymax (A): -30.50600 32.38900 zmin,zma (A): -4.013000 66.38100 x,y,z range (A): 55.55400 62.89500 70.39400 scale (grids/A): 2.275762 object centre (A): 8.970001 0.9414997 31.18400 number of atom coordinates read : 5223 total number of charged atoms : 4967 net assigned charge : 7.706048 assigned positive charge : 787.4264 centred at (gu) : 92.54086 93.17571 87.34954 assigned negative charge : -779.7256 centred at (gu) : 92.17505 93.31688 87.25491 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 223001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43844 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 98351 mr = 163528 m= 24092 mr = 76779 m= 3417 mr = 17063 m= 188 mr = 2052 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 89559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 39609 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) : 1.517175 object centre at (A) : 8.970001 0.9414997 31.18400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1456995 0.3926986 midg,1,midg; midg,igrid,midg -8.6801931E-02 -0.3134433 1,midg,midg; igrid,midg,midg -1.9172506E-02 0.1760263 gauss-seidel spectral radius is 0.9991686 estimated iterations to convergence 274 setup time was (sec) 1.480000 now iterating at: 14:12:36 rms-change max change #iterations 10.60454 276.7038 at 10iterations 6.070433 160.2155 at 20iterations 3.442952 70.01104 at 30iterations 1.949009 41.68228 at 40iterations 1.097641 22.72763 at 50iterations 0.6180821 12.03498 at 60iterations 0.3461661 7.260292 at 70iterations 0.1940971 3.602692 at 80iterations 0.1084115 1.962456 at 90iterations 6.0504958E-02 1.105965 at 100iterations 3.3823438E-02 0.6329269 at 110iterations 1.8855527E-02 0.3443165 at 120iterations 1.0540734E-02 0.2048416 at 130iterations 5.8730450E-03 0.1112022 at 140iterations 3.2715360E-03 6.8232536E-02 at 150iterations 1.8270243E-03 3.2375336E-02 at 160iterations 1.0246111E-03 1.8013000E-02 at 170iterations 5.7519350E-04 1.1301041E-02 at 180iterations finished qdiffx linear iterations at : 14:12:59 total time elapsed so far: 14.75000 # loops : 180 mean,max change (kT/e) : 5.7519350E-04 1.1301041E-02 energy calculations done at 14.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.88000 DelPhi exited at 14:13:00 14.884u 0.313s 0:26.41 57.5% 0+0k 0+0io 0pf+0w