Sat Oct 8 11:38:14 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 8 2011 at 11:38:14 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4142 !!! WARNING: HIR 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5142131 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): -1.532000 67.70000 ymin,ymax (A): -10.45500 39.12700 zmin,zma (A): -19.63700 45.11700 x,y,z range (A): 69.23199 49.58200 64.75400 scale (grids/A): 0.5142131 object centre (A): 33.08400 14.33600 12.74000 number of atom coordinates read : 4142 total number of charged atoms : 3977 net assigned charge : -7.985952 assigned positive charge : 619.5852 centred at (gu) : 88.05193 90.07121 90.32280 assigned negative charge : -627.5734 centred at (gu) : 88.11295 90.15252 90.38414 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6740 nv = 96 ne = 84 npr = 87368 no. pairs analyzed = 87368 no. exposed pairs = 4750 no. arc points = 31876 no. surface atoms = 1624 nbur = 2518 mkacc time = 0.1400000 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= 257 mr = 3720 m= 0 mr = 12 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3211 ## 452 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9218 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3380275E-11 -3.2492134E-10 midg,1,midg; midg,igrid,midg 7.6235969E-11 -3.5910019E-10 1,midg,midg; igrid,midg,midg 4.7586476E-11 -1.8022435E-10 gauss-seidel spectral radius is 0.9806020 estimated iterations to convergence 59 setup time was (sec) 0.5300000 now iterating at: 11:38:15 rms-change max change #iterations 6.6518895E-02 9.965988 at 10iterations 4.9962248E-03 0.7803054 at 20iterations 8.4234047E-04 0.1159143 at 30iterations 2.1572575E-04 3.4068108E-02 at 40iterations 5.9357390E-05 9.8152161E-03 at 50iterations finished qdiffx linear iterations at : 11:38:18 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 5.9357390E-05 9.8152161E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 11:38:19 4.180u 0.314s 0:04.83 92.9% 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 8 2011 at 11:38:19 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4142 !!! WARNING: HIR 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.542639 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): -1.532000 67.70000 ymin,ymax (A): -10.45500 39.12700 zmin,zma (A): -19.63700 45.11700 x,y,z range (A): 69.23199 49.58200 64.75400 scale (grids/A): 1.542639 object centre (A): 33.08400 14.33600 12.74000 number of atom coordinates read : 4142 total number of charged atoms : 3977 net assigned charge : -7.985952 assigned positive charge : 619.5852 centred at (gu) : 84.15469 90.21246 90.96716 assigned negative charge : -627.5734 centred at (gu) : 84.33829 90.45706 91.15183 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 77461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31876 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22807 mr = 55304 m= 2045 mr = 15728 m= 44 mr = 960 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1193 time to turn everything in is 0.4200000 number of dielectric boundary points 30363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 368 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 29988 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) : 0.5142131 object centre at (A) : 33.08400 14.33600 12.74000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0408230E-03 -1.2219416E-02 midg,1,midg; midg,igrid,midg -3.5511751E-03 -1.0807659E-02 1,midg,midg; igrid,midg,midg 1.6171312E-02 -7.5377990E-03 gauss-seidel spectral radius is 0.9980574 estimated iterations to convergence 180 setup time was (sec) 0.7100000 now iterating at: 11:38:20 rms-change max change #iterations 3.547339 164.5804 at 10iterations 1.430470 50.47733 at 20iterations 0.5812783 20.81930 at 30iterations 0.2355574 9.310619 at 40iterations 9.5677927E-02 3.142288 at 50iterations 3.9042164E-02 1.356014 at 60iterations 1.6012689E-02 0.6075058 at 70iterations 6.6324389E-03 0.2207870 at 80iterations 2.8281074E-03 0.1050074 at 90iterations 1.2652404E-03 4.3792725E-02 at 100iterations 6.1524857E-04 2.3206711E-02 at 110iterations 3.2811603E-04 1.1852264E-02 at 120iterations finished qdiffx linear iterations at : 11:38:29 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 3.2811603E-04 1.1852264E-02 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 11:38:29 9.727u 0.343s 0:10.37 97.0% 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 8 2011 at 11:38:29 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4142 !!! WARNING: HIR 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.313959 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): -1.532000 67.70000 ymin,ymax (A): -10.45500 39.12700 zmin,zma (A): -19.63700 45.11700 x,y,z range (A): 69.23199 49.58200 64.75400 scale (grids/A): 2.313959 object centre (A): 33.08400 14.33600 12.74000 number of atom coordinates read : 4142 total number of charged atoms : 3977 net assigned charge : -7.985952 assigned positive charge : 619.5852 centred at (gu) : 81.23179 90.31842 91.45042 assigned negative charge : -627.5734 centred at (gu) : 81.50729 90.68543 91.72754 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 180785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31876 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81743 mr = 135131 m= 21032 mr = 65408 m= 3121 mr = 15637 m= 189 mr = 1987 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 4021 time to turn everything in is 0.9900000 number of dielectric boundary points 68637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 31727 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) : 1.542639 object centre at (A) : 33.08400 14.33600 12.74000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2202625 -0.2268086 midg,1,midg; midg,igrid,midg -8.0731288E-02 -0.1715521 1,midg,midg; igrid,midg,midg 0.4830202 -0.3414547 gauss-seidel spectral radius is 0.9991150 estimated iterations to convergence 266 setup time was (sec) 1.310000 now iterating at: 11:38:31 rms-change max change #iterations 9.463161 252.6682 at 10iterations 5.289599 119.3051 at 20iterations 2.937314 65.90615 at 30iterations 1.625327 31.09304 at 40iterations 0.8951582 17.83467 at 50iterations 0.4925734 10.18525 at 60iterations 0.2703599 5.428191 at 70iterations 0.1479074 2.857263 at 80iterations 8.1276931E-02 1.711915 at 90iterations 4.4480149E-02 0.8448277 at 100iterations 2.4321893E-02 0.4918633 at 110iterations 1.3391153E-02 0.2584095 at 120iterations 7.3466683E-03 0.1644516 at 130iterations 4.0748832E-03 8.3286285E-02 at 140iterations 2.2753950E-03 4.4384003E-02 at 150iterations 1.2944420E-03 2.7675629E-02 at 160iterations 7.5922115E-04 1.5550077E-02 at 170iterations 4.6109231E-04 1.0320663E-02 at 180iterations finished qdiffx linear iterations at : 11:38:46 total time elapsed so far: 16.06000 # loops : 180 mean,max change (kT/e) : 4.6109231E-04 1.0320663E-02 energy calculations done at 16.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.19000 DelPhi exited at 11:38:46 16.194u 0.372s 0:16.87 98.1% 0+0k 0+0io 0pf+0w