Tue Oct 11 04:25:21 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 Tue Oct 11 2011 at 04:25:21 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: 352 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6502996 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): -14.65200 34.07500 ymin,ymax (A): 6.854000 55.12800 zmin,zma (A): 25.64700 80.39100 x,y,z range (A): 48.72700 48.27400 54.74400 scale (grids/A): 0.6502996 object centre (A): 9.711500 30.99100 53.01900 number of atom coordinates read : 2778 total number of charged atoms : 2625 net assigned charge : 2.154017 assigned positive charge : 423.8477 centred at (gu) : 89.70037 90.43880 88.21082 assigned negative charge : -421.6942 centred at (gu) : 90.02893 90.27464 88.21152 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7694 nv = 96 ne = 84 npr = 57759 no. pairs analyzed = 57759 no. exposed pairs = 3355 no. arc points = 23292 no. surface atoms = 1122 nbur = 1656 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 431 mr = 4336 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2100000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2288 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9249423E-09 2.7022899E-09 midg,1,midg; midg,igrid,midg -2.1675852E-08 3.3882493E-08 1,midg,midg; igrid,midg,midg 6.0577477E-08 -4.9402626E-08 gauss-seidel spectral radius is 0.9877558 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 04:25:22 rms-change max change #iterations 0.1665993 25.78964 at 10iterations 1.7456567E-02 2.354024 at 20iterations 1.9749687E-03 0.2596588 at 30iterations 2.9453458E-04 3.9302826E-02 at 40iterations 7.1176000E-05 7.6828003E-03 at 50iterations finished qdiffx linear iterations at : 04:25:25 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 7.1176000E-05 7.6828003E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 04:25:25 3.482u 0.180s 0:04.20 87.1% 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 Tue Oct 11 2011 at 04:25:25 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: 352 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.950899 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): -14.65200 34.07500 ymin,ymax (A): 6.854000 55.12800 zmin,zma (A): 25.64700 80.39100 x,y,z range (A): 48.72700 48.27400 54.74400 scale (grids/A): 1.950899 object centre (A): 9.711500 30.99100 53.01900 number of atom coordinates read : 2778 total number of charged atoms : 2625 net assigned charge : 2.154017 assigned positive charge : 423.8477 centred at (gu) : 89.10087 91.31590 84.63176 assigned negative charge : -421.6942 centred at (gu) : 90.08653 90.82395 84.63428 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23292 grid for indexing accessible points = 1.400000 m= 29799 mr = 58628 m= 4682 mr = 21932 m= 306 mr = 2827 m= 4 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 519 time to turn everything in is 0.4000000 number of dielectric boundary points 34359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20698 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) : 0.6502996 object centre at (A) : 9.711500 30.99100 53.01900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3633799E-03 -2.3045206E-02 midg,1,midg; midg,igrid,midg -1.6661653E-02 3.6262479E-02 1,midg,midg; igrid,midg,midg 7.0705310E-02 -1.8528787E-02 gauss-seidel spectral radius is 0.9987106 estimated iterations to convergence 221 setup time was (sec) 0.6200000 now iterating at: 04:25:26 rms-change max change #iterations 4.710328 199.9436 at 10iterations 2.261666 78.38362 at 20iterations 1.086662 35.61582 at 30iterations 0.5240098 15.71971 at 40iterations 0.2505307 7.840268 at 50iterations 0.1201308 3.622723 at 60iterations 5.7636369E-02 1.866024 at 70iterations 2.7749231E-02 0.8691483 at 80iterations 1.3310001E-02 0.4044685 at 90iterations 6.3576605E-03 0.1978340 at 100iterations 3.0599255E-03 9.6695423E-02 at 110iterations 1.4740181E-03 4.3123245E-02 at 120iterations finished qdiffx linear iterations at : 04:25:33 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.4740181E-03 4.3123245E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 04:25:34 7.777u 0.281s 0:08.56 94.0% 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 Tue Oct 11 2011 at 04:25:34 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: 352 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.926348 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): -14.65200 34.07500 ymin,ymax (A): 6.854000 55.12800 zmin,zma (A): 25.64700 80.39100 x,y,z range (A): 48.72700 48.27400 54.74400 scale (grids/A): 2.926348 object centre (A): 9.711500 30.99100 53.01900 number of atom coordinates read : 2778 total number of charged atoms : 2625 net assigned charge : 2.154017 assigned positive charge : 423.8477 centred at (gu) : 88.65113 91.97375 81.94762 assigned negative charge : -421.6942 centred at (gu) : 90.12957 91.23582 81.95129 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 192478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23292 grid for indexing accessible points = 1.400000 m= 97080 mr = 142191 m= 34568 mr = 79562 m= 8391 mr = 27615 m= 1343 mr = 6204 m= 109 mr = 859 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1805 time to turn everything in is 1.080000 number of dielectric boundary points 77480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 20991 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) : 1.950899 object centre at (A) : 9.711500 30.99100 53.01900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6348027E-02 -0.3404744 midg,1,midg; midg,igrid,midg -0.1813960 0.4408781 1,midg,midg; igrid,midg,midg 0.5743039 -6.2591709E-02 gauss-seidel spectral radius is 0.9992770 estimated iterations to convergence 293 setup time was (sec) 1.340000 now iterating at: 04:25:35 rms-change max change #iterations 10.89389 479.6901 at 10iterations 6.387900 157.7563 at 20iterations 3.732146 91.40794 at 30iterations 2.184718 42.52408 at 40iterations 1.273904 28.04783 at 50iterations 0.7406291 12.39890 at 60iterations 0.4310344 8.143313 at 70iterations 0.2501922 4.364069 at 80iterations 0.1454916 2.566303 at 90iterations 8.4260307E-02 1.449997 at 100iterations 4.8956834E-02 0.8133583 at 110iterations 2.8474694E-02 0.4751396 at 120iterations 1.6573973E-02 0.2635117 at 130iterations 9.6630305E-03 0.1566124 at 140iterations 5.6849257E-03 9.6054077E-02 at 150iterations 3.3748904E-03 6.2713623E-02 at 160iterations 2.0430996E-03 3.4968376E-02 at 170iterations 1.2663719E-03 2.2781372E-02 at 180iterations finished qdiffx linear iterations at : 04:25:47 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.2663719E-03 2.2781372E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 04:25:48 13.285u 0.212s 0:13.97 96.5% 0+0k 0+0io 0pf+0w