Sun Oct 9 12:26:02 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+sph.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 = amb.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 Sun Oct 9 2011 at 12:26:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 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: 0.6715587 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): -6.435000 43.89100 ymin,ymax (A): -14.25800 38.75300 zmin,zma (A): 3.169000 45.37800 x,y,z range (A): 50.32600 53.01100 42.20900 scale (grids/A): 0.6715587 object centre (A): 18.72800 12.24750 24.27350 number of atom coordinates read : 2390 total number of charged atoms : 2248 net assigned charge : 3.500023 assigned positive charge : 364.2080 centred at (gu) : 89.49828 90.51023 90.20407 assigned negative charge : -360.7085 centred at (gu) : 89.52916 90.68123 90.29640 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7140 nv = 96 ne = 84 npr = 48518 no. pairs analyzed = 48518 no. exposed pairs = 2963 no. arc points = 20936 no. surface atoms = 990 nbur = 1400 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3894 m= 3 mr = 60 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1957 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3464708E-08 -1.1021625E-08 midg,1,midg; midg,igrid,midg 4.8364754E-08 -3.3946446E-08 1,midg,midg; igrid,midg,midg 2.2109361E-08 4.3695496E-09 gauss-seidel spectral radius is 0.9884829 estimated iterations to convergence 76 setup time was (sec) 0.5400000 now iterating at: 12:26:03 rms-change max change #iterations 0.1721857 28.14292 at 10iterations 1.9364536E-02 2.573959 at 20iterations 2.4312558E-03 0.3267069 at 30iterations 4.8413308E-04 7.1069717E-02 at 40iterations 1.4213295E-04 2.1511078E-02 at 50iterations finished qdiffx linear iterations at : 12:26:06 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.4213295E-04 2.1511078E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 12:26:07 3.560u 0.185s 0:04.01 93.2% 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 Sun Oct 9 2011 at 12:26:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 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: 2.014676 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): -6.435000 43.89100 ymin,ymax (A): -14.25800 38.75300 zmin,zma (A): 3.169000 45.37800 x,y,z range (A): 50.32600 53.01100 42.20900 scale (grids/A): 2.014676 object centre (A): 18.72800 12.24750 24.27350 number of atom coordinates read : 2390 total number of charged atoms : 2248 net assigned charge : 3.500023 assigned positive charge : 364.2080 centred at (gu) : 88.49435 91.53024 90.61152 assigned negative charge : -360.7085 centred at (gu) : 88.58745 92.04331 90.88896 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 76465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20936 grid for indexing accessible points = 1.400000 m= 28301 mr = 53010 m= 4796 mr = 20771 m= 337 mr = 2961 m= 3 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.6100000 number of dielectric boundary points 33026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17757 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) : 0.6715587 object centre at (A) : 18.72800 12.24750 24.27350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4175517E-02 1.0985821E-02 midg,1,midg; midg,igrid,midg 2.0316677E-02 -4.8071090E-02 1,midg,midg; igrid,midg,midg 3.4464933E-02 -1.2075922E-02 gauss-seidel spectral radius is 0.9987542 estimated iterations to convergence 224 setup time was (sec) 0.9200000 now iterating at: 12:26:08 rms-change max change #iterations 4.515495 203.0590 at 10iterations 2.178238 69.78179 at 20iterations 1.055866 33.01061 at 30iterations 0.5120122 18.32696 at 40iterations 0.2474214 7.920100 at 50iterations 0.1200135 3.791283 at 60iterations 5.8211707E-02 1.868883 at 70iterations 2.8239472E-02 0.8615227 at 80iterations 1.3867095E-02 0.4492455 at 90iterations 6.8036239E-03 0.2154036 at 100iterations 3.3887553E-03 0.1093292 at 110iterations 1.7280377E-03 5.4996490E-02 at 120iterations finished qdiffx linear iterations at : 12:26:15 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.7280377E-03 5.4996490E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 12:26:15 8.154u 0.218s 0:08.67 96.4% 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 Sun Oct 9 2011 at 12:26:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 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: 3.022014 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): -6.435000 43.89100 ymin,ymax (A): -14.25800 38.75300 zmin,zma (A): 3.169000 45.37800 x,y,z range (A): 50.32600 53.01100 42.20900 scale (grids/A): 3.022014 object centre (A): 18.72800 12.24750 24.27350 number of atom coordinates read : 2390 total number of charged atoms : 2248 net assigned charge : 3.500023 assigned positive charge : 364.2080 centred at (gu) : 87.74132 92.29510 90.91720 assigned negative charge : -360.7085 centred at (gu) : 87.88110 93.06501 91.33337 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 176505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20936 grid for indexing accessible points = 1.400000 m= 91339 mr = 128264 m= 33679 mr = 74647 m= 8635 mr = 26793 m= 1476 mr = 6363 m= 97 mr = 1012 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 1.540000 number of dielectric boundary points 74610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 17979 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) : 2.014676 object centre at (A) : 18.72800 12.24750 24.27350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4108841 2.1050343E-02 midg,1,midg; midg,igrid,midg 0.4412823 -0.5632139 1,midg,midg; igrid,midg,midg 0.3738031 -0.2881636 gauss-seidel spectral radius is 0.9992784 estimated iterations to convergence 294 setup time was (sec) 1.880000 now iterating at: 12:26:17 rms-change max change #iterations 10.31430 407.6035 at 10iterations 6.038815 135.0588 at 20iterations 3.538111 72.94582 at 30iterations 2.070980 39.74037 at 40iterations 1.203966 22.94700 at 50iterations 0.7008373 12.87223 at 60iterations 0.4079807 7.602479 at 70iterations 0.2372424 4.634178 at 80iterations 0.1380543 2.792326 at 90iterations 8.0196708E-02 1.594585 at 100iterations 4.6650302E-02 0.7946148 at 110iterations 2.7184503E-02 0.5105362 at 120iterations 1.5963286E-02 0.2896805 at 130iterations 9.4439378E-03 0.1649742 at 140iterations 5.6942836E-03 0.1273756 at 150iterations 3.5461690E-03 6.9631577E-02 at 160iterations 2.3234279E-03 5.0048828E-02 at 170iterations 1.6121052E-03 3.5709381E-02 at 180iterations finished qdiffx linear iterations at : 12:26:30 total time elapsed so far: 14.69000 # loops : 180 mean,max change (kT/e) : 1.6121052E-03 3.5709381E-02 energy calculations done at 14.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.88000 DelPhi exited at 12:26:31 14.886u 0.213s 0:15.36 98.2% 0+0k 0+0io 0pf+0w