Wed Dec 28 11:03:10 PST 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 Wed Dec 28 2011 at 11:03:10 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6429939 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): -5.395000 33.95400 ymin,ymax (A): -3.505000 47.89900 zmin,zma (A): -7.990000 47.37600 x,y,z range (A): 39.34900 51.40400 55.36600 scale (grids/A): 0.6429939 object centre (A): 14.27950 22.19700 19.69300 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681010 assigned positive charge : 290.9500 centred at (gu) : 89.67825 92.57787 89.85477 assigned negative charge : -286.2693 centred at (gu) : 89.58575 92.70908 89.92436 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5531 nv = 96 ne = 84 npr = 40274 no. pairs analyzed = 40274 no. exposed pairs = 2480 no. arc points = 17141 no. surface atoms = 837 nbur = 1122 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 272 mr = 3073 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3600000 number of dielectric boundary points 2699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1693 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 6482 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4589921E-08 1.2414559E-09 midg,1,midg; midg,igrid,midg 1.1494954E-08 -8.4710425E-09 1,midg,midg; igrid,midg,midg -9.8261010E-10 1.5163005E-08 gauss-seidel spectral radius is 0.9874109 estimated iterations to convergence 73 setup time was (sec) 0.7700000 now iterating at: 11:03:11 rms-change max change #iterations 0.1292939 21.93158 at 10iterations 1.2805291E-02 2.431141 at 20iterations 1.2709617E-03 0.2076721 at 30iterations 1.2637551E-04 1.8825531E-02 at 40iterations 1.2456931E-05 2.1190643E-03 at 50iterations finished qdiffx linear iterations at : 11:03:18 total time elapsed so far: 7.320000 # loops : 50 mean,max change (kT/e) : 1.2456931E-05 2.1190643E-03 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 11:03:19 7.542u 0.702s 0:08.56 96.2% 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 Wed Dec 28 2011 at 11:03:19 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.928982 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): -5.395000 33.95400 ymin,ymax (A): -3.505000 47.89900 zmin,zma (A): -7.990000 47.37600 x,y,z range (A): 39.34900 51.40400 55.36600 scale (grids/A): 1.928982 object centre (A): 14.27950 22.19700 19.69300 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681010 assigned positive charge : 290.9500 centred at (gu) : 89.03474 97.73350 89.56435 assigned negative charge : -286.2693 centred at (gu) : 88.75749 98.12711 89.77319 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 59810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17141 grid for indexing accessible points = 1.400000 m= 21299 mr = 41363 m= 3006 mr = 16103 m= 141 mr = 1913 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2320 time to turn everything in is 0.7000000 number of dielectric boundary points 24821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14394 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) : 0.6429939 object centre at (A) : 14.27950 22.19700 19.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3528137E-02 3.6991488E-02 midg,1,midg; midg,igrid,midg 3.3596892E-02 -8.4070656E-03 1,midg,midg; igrid,midg,midg 7.5881807E-03 8.2491320E-03 gauss-seidel spectral radius is 0.9985901 estimated iterations to convergence 211 setup time was (sec) 1.190000 now iterating at: 11:03:21 rms-change max change #iterations 3.733464 177.2384 at 10iterations 1.728686 59.36696 at 20iterations 0.8038995 27.59921 at 30iterations 0.3705930 12.40888 at 40iterations 0.1709614 5.921748 at 50iterations 7.8883290E-02 2.572198 at 60iterations 3.6383465E-02 1.278746 at 70iterations 1.6861374E-02 0.6233015 at 80iterations 7.7824015E-03 0.2758188 at 90iterations 3.6109209E-03 0.1357327 at 100iterations 1.6704727E-03 5.4843903E-02 at 110iterations 7.7278598E-04 2.5936127E-02 at 120iterations finished qdiffx linear iterations at : 11:03:36 total time elapsed so far: 16.25000 # loops : 120 mean,max change (kT/e) : 7.7278598E-04 2.5936127E-02 energy calculations done at 16.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.47000 DelPhi exited at 11:03:37 16.471u 0.804s 0:17.85 96.7% 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 Wed Dec 28 2011 at 11:03:37 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.893472 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): -5.395000 33.95400 ymin,ymax (A): -3.505000 47.89900 zmin,zma (A): -7.990000 47.37600 x,y,z range (A): 39.34900 51.40400 55.36600 scale (grids/A): 2.893472 object centre (A): 14.27950 22.19700 19.69300 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681010 assigned positive charge : 290.9500 centred at (gu) : 88.55206 101.6003 89.34653 assigned negative charge : -286.2693 centred at (gu) : 88.13628 102.1908 89.65985 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 138177 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17141 grid for indexing accessible points = 1.400000 m= 69915 mr = 100093 m= 24550 mr = 57954 m= 5309 mr = 20241 m= 660 mr = 4018 m= 23 mr = 488 m= 0 mr = 6 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 8109 time to turn everything in is 1.640000 number of dielectric boundary points 55834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 14606 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) : 1.928982 object centre at (A) : 14.27950 22.19700 19.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0739530E-03 0.9460785 midg,1,midg; midg,igrid,midg 0.3806603 -0.1267753 1,midg,midg; igrid,midg,midg 0.1390042 4.6872344E-02 gauss-seidel spectral radius is 0.9992336 estimated iterations to convergence 285 setup time was (sec) 2.160000 now iterating at: 11:03:39 rms-change max change #iterations 8.750201 388.4424 at 10iterations 5.035338 124.7212 at 20iterations 2.876505 81.53361 at 30iterations 1.638826 40.30029 at 40iterations 0.9337851 21.78855 at 50iterations 0.5320767 11.70789 at 60iterations 0.3020393 6.199795 at 70iterations 0.1717250 3.721945 at 80iterations 9.7632580E-02 1.888190 at 90iterations 5.5437826E-02 1.092272 at 100iterations 3.1456888E-02 0.5986061 at 110iterations 1.7900512E-02 0.3789754 at 120iterations 1.0157086E-02 0.2039490 at 130iterations 5.7662227E-03 0.1214838 at 140iterations 3.2741816E-03 6.9698334E-02 at 150iterations 1.8624010E-03 3.6543608E-02 at 160iterations 1.0566942E-03 2.3330688E-02 at 170iterations 6.0057174E-04 1.1710644E-02 at 180iterations finished qdiffx linear iterations at : 11:04:04 total time elapsed so far: 27.02000 # loops : 180 mean,max change (kT/e) : 6.0057174E-04 1.1710644E-02 energy calculations done at 27.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.25000 DelPhi exited at 11:04:05 27.259u 0.691s 0:28.46 98.1% 0+0k 0+0io 0pf+0w