Mon Oct 10 14:07:24 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 Mon Oct 10 2011 at 14:07:24 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 0.7232685 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): -23.34600 25.87500 ymin,ymax (A): -23.13300 21.05400 zmin,zma (A): -24.03900 20.34600 x,y,z range (A): 49.22100 44.18700 44.38500 scale (grids/A): 0.7232685 object centre (A): 1.264500 -1.039501 -1.846500 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : -1.499990 assigned positive charge : 282.5172 centred at (gu) : 89.57944 90.48591 90.99504 assigned negative charge : -284.0172 centred at (gu) : 89.43066 90.24667 91.04749 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6902 nv = 96 ne = 84 npr = 40649 no. pairs analyzed = 40649 no. exposed pairs = 2417 no. arc points = 17911 no. surface atoms = 809 nbur = 1133 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 3733 m= 2 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.2500000 number of dielectric boundary points 3559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1483 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2343824E-08 -6.2326222E-08 midg,1,midg; midg,igrid,midg -1.5789203E-07 1.4367414E-07 1,midg,midg; igrid,midg,midg -1.2356243E-07 6.9185027E-08 gauss-seidel spectral radius is 0.9900277 estimated iterations to convergence 81 setup time was (sec) 0.4800000 now iterating at: 14:07:25 rms-change max change #iterations 0.2134985 29.26578 at 10iterations 2.7434610E-02 3.232854 at 20iterations 3.5512242E-03 0.5055885 at 30iterations 4.4378045E-04 6.3686550E-02 at 40iterations 5.7873785E-05 7.7695847E-03 at 50iterations finished qdiffx linear iterations at : 14:07:27 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 5.7873785E-05 7.7695847E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 14:07:28 3.259u 0.205s 0:03.77 91.5% 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 Mon Oct 10 2011 at 14:07:28 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 2.169806 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): -23.34600 25.87500 ymin,ymax (A): -23.13300 21.05400 zmin,zma (A): -24.03900 20.34600 x,y,z range (A): 49.22100 44.18700 44.38500 scale (grids/A): 2.169806 object centre (A): 1.264500 -1.039501 -1.846500 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : -1.499990 assigned positive charge : 282.5172 centred at (gu) : 88.73835 91.45786 92.98518 assigned negative charge : -284.0172 centred at (gu) : 88.29205 90.74012 93.14265 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72504 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17911 grid for indexing accessible points = 1.400000 m= 27915 mr = 49016 m= 6036 mr = 20741 m= 726 mr = 4188 m= 21 mr = 428 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 6283 time to turn everything in is 0.5400000 number of dielectric boundary points 32827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14405 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) : 0.7232685 object centre at (A) : 1.264500 -1.039501 -1.846500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5790831E-02 -3.5471156E-02 midg,1,midg; midg,igrid,midg -1.0564655E-02 4.9184885E-02 1,midg,midg; igrid,midg,midg -6.4242274E-02 9.5300646E-03 gauss-seidel spectral radius is 0.9988735 estimated iterations to convergence 236 setup time was (sec) 0.8100000 now iterating at: 14:07:29 rms-change max change #iterations 4.573671 197.0592 at 10iterations 2.285055 80.86621 at 20iterations 1.143933 44.03727 at 30iterations 0.5748444 18.23318 at 40iterations 0.2889692 9.390724 at 50iterations 0.1442927 4.264767 at 60iterations 7.2619751E-02 2.409599 at 70iterations 3.6313143E-02 1.094009 at 80iterations 1.8200802E-02 0.5173709 at 90iterations 9.1464734E-03 0.2510300 at 100iterations 4.5818444E-03 0.1475940 at 110iterations 2.2996240E-03 6.8981171E-02 at 120iterations finished qdiffx linear iterations at : 14:07:35 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 2.2996240E-03 6.8981171E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 14:07:36 7.466u 0.221s 0:08.24 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 Mon Oct 10 2011 at 14:07:36 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.254708 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): -23.34600 25.87500 ymin,ymax (A): -23.13300 21.05400 zmin,zma (A): -24.03900 20.34600 x,y,z range (A): 49.22100 44.18700 44.38500 scale (grids/A): 3.254708 object centre (A): 1.264500 -1.039501 -1.846500 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : -1.499990 assigned positive charge : 282.5172 centred at (gu) : 88.10754 92.18689 94.47796 assigned negative charge : -284.0172 centred at (gu) : 87.43804 91.11008 94.71392 start vw surface at 0.1500000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 167173 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17911 grid for indexing accessible points = 1.400000 m= 85643 mr = 118257 m= 36378 mr = 70238 m= 11811 mr = 29912 m= 2916 mr = 9337 m= 395 mr = 2255 m= 21 mr = 255 m= 0 mr = 7 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 20575 time to turn everything in is 1.690000 number of dielectric boundary points 74076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 14480 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) : 2.169806 object centre at (A) : 1.264500 -1.039501 -1.846500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4288801 -0.3839164 midg,1,midg; midg,igrid,midg -5.6748219E-02 0.4615012 1,midg,midg; igrid,midg,midg -0.6751460 -9.6124530E-02 gauss-seidel spectral radius is 0.9993017 estimated iterations to convergence 299 setup time was (sec) 2.000000 now iterating at: 14:07:38 rms-change max change #iterations 9.926581 331.0326 at 10iterations 5.827065 125.5023 at 20iterations 3.397490 61.67573 at 30iterations 1.983874 33.48220 at 40iterations 1.159715 20.65461 at 50iterations 0.6754946 11.60392 at 60iterations 0.3935920 6.328570 at 70iterations 0.2295960 4.001358 at 80iterations 0.1338072 2.255260 at 90iterations 7.8267634E-02 1.348446 at 100iterations 4.5393959E-02 0.7848282 at 110iterations 2.6443804E-02 0.4930778 at 120iterations 1.5425833E-02 0.2689667 at 130iterations 8.9899004E-03 0.1573257 at 140iterations 5.2584428E-03 9.5594406E-02 at 150iterations 3.0551436E-03 5.0399780E-02 at 160iterations 1.7826388E-03 3.0696392E-02 at 170iterations 1.0417015E-03 1.8357277E-02 at 180iterations finished qdiffx linear iterations at : 14:07:49 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 1.0417015E-03 1.8357277E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 14:07:49 12.514u 0.229s 0:13.06 97.4% 0+0k 0+0io 0pf+0w