Sat Oct 8 15:20:46 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 15:20:46 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 !!! WARNING: SEP 64 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5723473 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): -7.513000 48.75300 ymin,ymax (A): -11.92100 38.60100 zmin,zma (A): -7.814000 54.38600 x,y,z range (A): 56.26600 50.52200 62.20000 scale (grids/A): 0.5723473 object centre (A): 20.62000 13.34000 23.28600 number of atom coordinates read : 3202 total number of charged atoms : 3056 net assigned charge : 2.025007 assigned positive charge : 477.8068 centred at (gu) : 88.98273 89.56525 89.46306 assigned negative charge : -475.7831 centred at (gu) : 88.91695 89.53054 89.50201 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6850 nv = 96 ne = 84 npr = 66047 no. pairs analyzed = 66047 no. exposed pairs = 3816 no. arc points = 26504 no. surface atoms = 1269 nbur = 1933 mkacc time = 0.1700000 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 = 1.512000 m= 274 mr = 3756 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3600000 number of dielectric boundary points 3344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2700 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2001306E-09 -3.1599265E-10 midg,1,midg; midg,igrid,midg -3.1736724E-10 8.8386182E-10 1,midg,midg; igrid,midg,midg -1.1014734E-09 1.2083216E-09 gauss-seidel spectral radius is 0.9842615 estimated iterations to convergence 65 setup time was (sec) 0.6400000 now iterating at: 15:20:47 rms-change max change #iterations 9.4549157E-02 14.29827 at 10iterations 7.3898118E-03 1.013033 at 20iterations 5.7227974E-04 8.4075928E-02 at 30iterations 4.8031950E-05 7.0705414E-03 at 40iterations 4.9808732E-06 7.1716309E-04 at 50iterations finished qdiffx linear iterations at : 15:20:52 total time elapsed so far: 4.970000 # loops : 50 mean,max change (kT/e) : 4.9808732E-06 7.1716309E-04 energy calculations done at 4.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.150000 DelPhi exited at 15:20:52 5.152u 0.462s 0:05.89 95.2% 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 8 2011 at 15:20:52 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 !!! WARNING: SEP 64 has a net charge of -0.4750 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: 1.717042 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): -7.513000 48.75300 ymin,ymax (A): -11.92100 38.60100 zmin,zma (A): -7.814000 54.38600 x,y,z range (A): 56.26600 50.52200 62.20000 scale (grids/A): 1.717042 object centre (A): 20.62000 13.34000 23.28600 number of atom coordinates read : 3202 total number of charged atoms : 3056 net assigned charge : 2.025007 assigned positive charge : 477.8068 centred at (gu) : 86.94732 88.69498 88.38826 assigned negative charge : -475.7831 centred at (gu) : 86.75041 88.59158 88.50560 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26504 grid for indexing accessible points = 1.400000 m= 25116 mr = 53242 m= 2939 mr = 17946 m= 101 mr = 1666 m= 0 mr = 34 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2384 time to turn everything in is 0.6300000 number of dielectric boundary points 30982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 23673 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) : 0.5723473 object centre at (A) : 20.62000 13.34000 23.28600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3377342E-02 8.4550921E-03 midg,1,midg; midg,igrid,midg 5.3166789E-03 6.2384699E-03 1,midg,midg; igrid,midg,midg -5.9474548E-03 5.4361108E-03 gauss-seidel spectral radius is 0.9983842 estimated iterations to convergence 197 setup time was (sec) 0.9600000 now iterating at: 15:20:54 rms-change max change #iterations 3.816225 151.6479 at 10iterations 1.667455 61.28270 at 20iterations 0.7320063 25.68200 at 30iterations 0.3210480 10.64871 at 40iterations 0.1408319 4.901557 at 50iterations 6.1957918E-02 1.886946 at 60iterations 2.7089436E-02 0.8818693 at 70iterations 1.1915214E-02 0.3688202 at 80iterations 5.2100685E-03 0.1815434 at 90iterations 2.2934503E-03 7.1681023E-02 at 100iterations 1.0063371E-03 3.1238556E-02 at 110iterations 4.4481357E-04 1.4194012E-02 at 120iterations finished qdiffx linear iterations at : 15:21:05 total time elapsed so far: 12.23000 # loops : 120 mean,max change (kT/e) : 4.4481357E-04 1.4194012E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 15:21:06 12.402u 0.504s 0:13.19 97.8% 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 15:21:06 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 !!! WARNING: SEP 64 has a net charge of -0.4750 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: 2.575563 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): -7.513000 48.75300 ymin,ymax (A): -11.92100 38.60100 zmin,zma (A): -7.814000 54.38600 x,y,z range (A): 56.26600 50.52200 62.20000 scale (grids/A): 2.575563 object centre (A): 20.62000 13.34000 23.28600 number of atom coordinates read : 3202 total number of charged atoms : 3056 net assigned charge : 2.025007 assigned positive charge : 477.8068 centred at (gu) : 85.42077 88.04217 87.58230 assigned negative charge : -475.7831 centred at (gu) : 85.12553 87.88727 87.75844 start vw surface at 0.1300000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 175973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26504 grid for indexing accessible points = 1.400000 m= 85318 mr = 129599 m= 26400 mr = 69157 m= 4748 mr = 20492 m= 440 mr = 3430 m= 22 mr = 272 m= 0 mr = 11 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 7797 time to turn everything in is 1.560000 number of dielectric boundary points 69940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 24437 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) : 1.717042 object centre at (A) : 20.62000 13.34000 23.28600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3202469 9.4783269E-03 midg,1,midg; midg,igrid,midg 0.1028715 8.1434138E-02 1,midg,midg; igrid,midg,midg -3.8791769E-03 3.2228626E-02 gauss-seidel spectral radius is 0.9991997 estimated iterations to convergence 279 setup time was (sec) 1.950000 now iterating at: 15:21:08 rms-change max change #iterations 9.489706 292.5472 at 10iterations 5.391117 144.0774 at 20iterations 3.054111 65.02881 at 30iterations 1.726622 34.74107 at 40iterations 0.9748704 18.44543 at 50iterations 0.5495920 10.68706 at 60iterations 0.3094969 6.216875 at 70iterations 0.1740824 3.405108 at 80iterations 9.7942054E-02 1.914835 at 90iterations 5.5081606E-02 1.072982 at 100iterations 3.0966995E-02 0.5719652 at 110iterations 1.7370813E-02 0.3131495 at 120iterations 9.7744651E-03 0.2193890 at 130iterations 5.5076880E-03 0.1046600 at 140iterations 3.0968310E-03 5.5966377E-02 at 150iterations 1.7506664E-03 3.4278870E-02 at 160iterations 9.9000928E-04 1.9260406E-02 at 170iterations 5.6458014E-04 1.1435509E-02 at 180iterations finished qdiffx linear iterations at : 15:21:26 total time elapsed so far: 19.55000 # loops : 180 mean,max change (kT/e) : 5.6458014E-04 1.1435509E-02 energy calculations done at 19.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.71000 DelPhi exited at 15:21:26 19.716u 0.524s 0:20.53 98.5% 0+0k 0+0io 0pf+0w