Mon Oct 10 14:37:12 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 14:37:12 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7397096 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): -20.67200 24.28200 ymin,ymax (A): -7.896000 35.84200 zmin,zma (A): -3.473000 44.65400 x,y,z range (A): 44.95400 43.73800 48.12700 scale (grids/A): 0.7397096 object centre (A): 1.805000 13.97300 20.59050 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 88.90747 90.55901 90.05443 assigned negative charge : -322.8520 centred at (gu) : 88.94582 90.63647 90.21478 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7890 nv = 96 ne = 84 npr = 43663 no. pairs analyzed = 43663 no. exposed pairs = 2716 no. arc points = 19060 no. surface atoms = 925 nbur = 1190 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 525 mr = 4352 m= 5 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.1600000 number of dielectric boundary points 3973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1546 ## 115 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 8358 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5362907E-08 -2.7315454E-07 midg,1,midg; midg,igrid,midg -2.4361972E-08 -2.0426056E-07 1,midg,midg; igrid,midg,midg -7.9570214E-08 -1.1788023E-07 gauss-seidel spectral radius is 0.9904764 estimated iterations to convergence 83 setup time was (sec) 0.3500000 now iterating at: 14:37:13 rms-change max change #iterations 0.2461533 33.44634 at 10iterations 3.2844573E-02 4.501291 at 20iterations 4.3605585E-03 0.6248817 at 30iterations 5.9532991E-04 7.3882103E-02 at 40iterations 8.0162987E-05 1.0986328E-02 at 50iterations finished qdiffx linear iterations at : 14:37:16 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 8.0162987E-05 1.0986328E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 14:37:16 3.307u 0.177s 0:03.96 87.6% 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 14:37:16 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 2.219129 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): -20.67200 24.28200 ymin,ymax (A): -7.896000 35.84200 zmin,zma (A): -3.473000 44.65400 x,y,z range (A): 44.95400 43.73800 48.12700 scale (grids/A): 2.219129 object centre (A): 1.805000 13.97300 20.59050 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 86.72218 91.67712 90.16336 assigned negative charge : -322.8520 centred at (gu) : 86.83753 91.90958 90.64414 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19060 grid for indexing accessible points = 1.400000 m= 32774 mr = 57275 m= 7053 mr = 24794 m= 840 mr = 4898 m= 32 mr = 471 m= 0 mr = 9 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1633 time to turn everything in is 0.4100000 number of dielectric boundary points 36516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15736 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) : 0.7397096 object centre at (A) : 1.805000 13.97300 20.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2616223E-02 -0.1336289 midg,1,midg; midg,igrid,midg -2.2750396E-02 -3.2308664E-02 1,midg,midg; igrid,midg,midg -1.3286014E-02 -6.4649931E-03 gauss-seidel spectral radius is 0.9989257 estimated iterations to convergence 241 setup time was (sec) 0.6300000 now iterating at: 14:37:17 rms-change max change #iterations 5.074991 194.5913 at 10iterations 2.566165 80.26320 at 20iterations 1.309264 37.36237 at 30iterations 0.6685822 19.88247 at 40iterations 0.3391169 9.462120 at 50iterations 0.1731314 5.220302 at 60iterations 8.8315994E-02 2.787317 at 70iterations 4.4837791E-02 1.209383 at 80iterations 2.2871196E-02 0.6086807 at 90iterations 1.1669841E-02 0.3391991 at 100iterations 5.9483391E-03 0.1580823 at 110iterations 3.0286345E-03 8.3160400E-02 at 120iterations finished qdiffx linear iterations at : 14:37:24 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 3.0286345E-03 8.3160400E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 14:37:25 7.839u 0.202s 0:08.34 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 Mon Oct 10 2011 at 14:37:25 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.328693 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): -20.67200 24.28200 ymin,ymax (A): -7.896000 35.84200 zmin,zma (A): -3.473000 44.65400 x,y,z range (A): 44.95400 43.73800 48.12700 scale (grids/A): 3.328693 object centre (A): 1.805000 13.97300 20.59050 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 85.08318 92.51556 90.24501 assigned negative charge : -322.8520 centred at (gu) : 85.25626 92.86446 90.96618 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 191791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19060 grid for indexing accessible points = 1.400000 m= 100757 mr = 138366 m= 42664 mr = 83102 m= 13703 mr = 35306 m= 3307 mr = 10880 m= 493 mr = 2550 m= 39 mr = 340 m= 0 mr = 12 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 5823 time to turn everything in is 1.280000 number of dielectric boundary points 82198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 15808 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) : 2.219129 object centre at (A) : 1.805000 13.97300 20.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5360967E-02 -1.273673 midg,1,midg; midg,igrid,midg -0.2099879 -0.1920529 1,midg,midg; igrid,midg,midg -0.2353839 -8.7221414E-02 gauss-seidel spectral radius is 0.9993172 estimated iterations to convergence 302 setup time was (sec) 1.510000 now iterating at: 14:37:26 rms-change max change #iterations 10.93179 337.4178 at 10iterations 6.433783 126.5702 at 20iterations 3.789259 64.58533 at 30iterations 2.226761 38.37897 at 40iterations 1.310769 22.27208 at 50iterations 0.7693799 12.98700 at 60iterations 0.4523377 7.353861 at 70iterations 0.2653788 4.869340 at 80iterations 0.1559157 2.552596 at 90iterations 9.1502026E-02 1.490411 at 100iterations 5.3599924E-02 0.8487911 at 110iterations 3.1418551E-02 0.5489125 at 120iterations 1.8464835E-02 0.3033180 at 130iterations 1.0842531E-02 0.1656952 at 140iterations 6.3586393E-03 9.8865032E-02 at 150iterations 3.7268372E-03 5.8271885E-02 at 160iterations 2.1926500E-03 3.8437843E-02 at 170iterations 1.2821141E-03 2.1282196E-02 at 180iterations finished qdiffx linear iterations at : 14:37:38 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 1.2821141E-03 2.1282196E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 14:37:38 12.923u 0.207s 0:13.50 97.1% 0+0k 0+0io 0pf+0w