Sat Oct 8 11:32:56 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 Sat Oct 8 2011 at 11:32:57 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3467 !!! WARNING: ALA 1069 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5302985 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): -16.18600 39.01400 ymin,ymax (A): -19.74200 34.91400 zmin,zma (A): -47.08000 20.05200 x,y,z range (A): 55.20000 54.65600 67.13200 scale (grids/A): 0.5302985 object centre (A): 11.41400 7.586000 -13.51400 number of atom coordinates read : 3467 total number of charged atoms : 3355 net assigned charge : 0.2280158 assigned positive charge : 523.5702 centred at (gu) : 91.23688 89.30296 89.08671 assigned negative charge : -523.3439 centred at (gu) : 91.22280 89.23777 88.97552 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6523 nv = 96 ne = 84 npr = 66666 no. pairs analyzed = 66666 no. exposed pairs = 4795 no. arc points = 33779 no. surface atoms = 1613 nbur = 1854 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 266 mr = 3141 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3403 ## 440 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8566 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9204702E-10 3.8064665E-10 midg,1,midg; midg,igrid,midg -3.1903929E-10 2.4209362E-10 1,midg,midg; igrid,midg,midg -3.3427545E-11 1.0194945E-10 gauss-seidel spectral radius is 0.9817284 estimated iterations to convergence 61 setup time was (sec) 0.6000000 now iterating at: 11:32:57 rms-change max change #iterations 6.5177962E-02 11.84488 at 10iterations 4.0367362E-03 0.6766930 at 20iterations 2.4950490E-04 4.1678429E-02 at 30iterations 1.6202477E-05 2.7709007E-03 at 40iterations 1.2417690E-06 1.6403198E-04 at 50iterations finished qdiffx linear iterations at : 11:33:00 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.2417690E-06 1.6403198E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 11:33:01 3.516u 0.151s 0:03.98 91.9% 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 Sat Oct 8 2011 at 11:33:01 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3467 !!! WARNING: ALA 1069 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.590896 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): -16.18600 39.01400 ymin,ymax (A): -19.74200 34.91400 zmin,zma (A): -47.08000 20.05200 x,y,z range (A): 55.20000 54.65600 67.13200 scale (grids/A): 1.590896 object centre (A): 11.41400 7.586000 -13.51400 number of atom coordinates read : 3467 total number of charged atoms : 3355 net assigned charge : 0.2280158 assigned positive charge : 523.5702 centred at (gu) : 93.70954 87.90824 87.25871 assigned negative charge : -523.3439 centred at (gu) : 93.66807 87.71301 86.92620 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21776 mr = 47318 m= 2418 mr = 14223 m= 47 mr = 1175 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 33863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 366 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25574 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) : 0.5302985 object centre at (A) : 11.41400 7.586000 -13.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0849835E-02 -5.7478501E-03 midg,1,midg; midg,igrid,midg -2.0555470E-03 2.8843693E-03 1,midg,midg; igrid,midg,midg 2.7044017E-03 2.8545042E-03 gauss-seidel spectral radius is 0.9981418 estimated iterations to convergence 184 setup time was (sec) 0.8600000 now iterating at: 11:33:02 rms-change max change #iterations 3.445115 160.3762 at 10iterations 1.419827 52.29159 at 20iterations 0.5865780 22.18348 at 30iterations 0.2417670 9.031208 at 40iterations 0.1000824 3.629593 at 50iterations 4.1117650E-02 1.573656 at 60iterations 1.7046917E-02 0.6089363 at 70iterations 7.0254710E-03 0.2378254 at 80iterations 2.9075593E-03 0.1069012 at 90iterations 1.1976915E-03 4.2734146E-02 at 100iterations 4.9537007E-04 1.6311646E-02 at 110iterations 2.0490051E-04 8.0146790E-03 at 120iterations finished qdiffx linear iterations at : 11:33:08 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 2.0490051E-04 8.0146790E-03 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 11:33:09 7.562u 0.192s 0:08.10 95.6% 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 Sat Oct 8 2011 at 11:33:09 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3467 !!! WARNING: ALA 1069 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.386343 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): -16.18600 39.01400 ymin,ymax (A): -19.74200 34.91400 zmin,zma (A): -47.08000 20.05200 x,y,z range (A): 55.20000 54.65600 67.13200 scale (grids/A): 2.386343 object centre (A): 11.41400 7.586000 -13.51400 number of atom coordinates read : 3467 total number of charged atoms : 3355 net assigned charge : 0.2280158 assigned positive charge : 523.5702 centred at (gu) : 95.56438 86.86211 85.88797 assigned negative charge : -523.3439 centred at (gu) : 95.50188 86.56936 85.38924 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 167878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 75156 mr = 116266 m= 21290 mr = 57644 m= 3811 mr = 15441 m= 239 mr = 2506 m= 4 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 76430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 26798 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) : 1.590896 object centre at (A) : 11.41400 7.586000 -13.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5138735 -0.1025901 midg,1,midg; midg,igrid,midg -9.6522551E-03 2.1173013E-02 1,midg,midg; igrid,midg,midg 6.0457669E-02 4.5512844E-02 gauss-seidel spectral radius is 0.9991437 estimated iterations to convergence 270 setup time was (sec) 1.660000 now iterating at: 11:33:11 rms-change max change #iterations 9.252752 270.1058 at 10iterations 5.320678 151.1916 at 20iterations 3.019005 75.82800 at 30iterations 1.698422 50.45028 at 40iterations 0.9470807 21.22975 at 50iterations 0.5286914 12.67009 at 60iterations 0.2945242 6.890679 at 70iterations 0.1631657 3.897003 at 80iterations 9.0226404E-02 2.379670 at 90iterations 4.9868252E-02 1.220698 at 100iterations 2.7545912E-02 0.5861340 at 110iterations 1.5203486E-02 0.2987118 at 120iterations 8.3603123E-03 0.1629858 at 130iterations 4.6104649E-03 9.0647697E-02 at 140iterations 2.5389395E-03 4.7795296E-02 at 150iterations 1.3956475E-03 2.7479023E-02 at 160iterations 7.7008194E-04 1.5609741E-02 at 170iterations 4.2405882E-04 9.6931458E-03 at 180iterations finished qdiffx linear iterations at : 11:33:21 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 4.2405882E-04 9.6931458E-03 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 11:33:21 12.143u 0.188s 0:12.64 97.4% 0+0k 0+0io 0pf+0w