Sat Oct 8 17:48:59 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 Sat Oct 8 2011 at 17:48:59 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3531 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 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: 0.5250350 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): -0.8420000 44.60500 ymin,ymax (A): -30.65400 26.10800 zmin,zma (A): 1.427000 69.23200 x,y,z range (A): 45.44700 56.76200 67.80500 scale (grids/A): 0.5250350 object centre (A): 21.88150 -2.273001 35.32950 number of atom coordinates read : 3531 total number of charged atoms : 3384 net assigned charge : -5.871982 assigned positive charge : 542.8039 centred at (gu) : 90.47767 91.83878 90.65636 assigned negative charge : -548.6779 centred at (gu) : 90.44035 91.79392 90.64870 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6164 nv = 96 ne = 84 npr = 72199 no. pairs analyzed = 72199 no. exposed pairs = 4198 no. arc points = 28899 no. surface atoms = 1426 nbur = 2105 mkacc time = 0.2000000 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= 224 mr = 3302 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2966 ## 449 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8234 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5887378E-10 -1.5515657E-10 midg,1,midg; midg,igrid,midg -2.0280407E-10 8.2814172E-12 1,midg,midg; igrid,midg,midg -2.6137709E-10 -2.7606009E-11 gauss-seidel spectral radius is 0.9813477 estimated iterations to convergence 60 setup time was (sec) 0.7100000 now iterating at: 17:49:00 rms-change max change #iterations 6.8044327E-02 10.75028 at 10iterations 4.1853697E-03 0.6428604 at 20iterations 3.7555787E-04 6.9609761E-02 at 30iterations 8.0257698E-05 1.6910315E-02 at 40iterations 2.1046477E-05 4.4125319E-03 at 50iterations finished qdiffx linear iterations at : 17:49:03 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 2.1046477E-05 4.4125319E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 17:49:04 4.321u 0.284s 0:04.87 94.4% 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 17:49:04 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3531 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.575105 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): -0.8420000 44.60500 ymin,ymax (A): -30.65400 26.10800 zmin,zma (A): 1.427000 69.23200 x,y,z range (A): 45.44700 56.76200 67.80500 scale (grids/A): 1.575105 object centre (A): 21.88150 -2.273001 35.32950 number of atom coordinates read : 3531 total number of charged atoms : 3384 net assigned charge : -5.871982 assigned positive charge : 542.8039 centred at (gu) : 91.43207 95.51513 91.96799 assigned negative charge : -548.6779 centred at (gu) : 91.32069 95.38101 91.94586 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 69668 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28899 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20810 mr = 48714 m= 1851 mr = 14241 m= 51 mr = 845 m= 0 mr = 6 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 28574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 409 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 25671 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) : 0.5250350 object centre at (A) : 21.88150 -2.273001 35.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2750296E-03 1.1823767E-02 midg,1,midg; midg,igrid,midg -8.0500329E-03 -1.1055669E-02 1,midg,midg; igrid,midg,midg -4.3770899E-03 1.2430275E-03 gauss-seidel spectral radius is 0.9980846 estimated iterations to convergence 182 setup time was (sec) 0.9400000 now iterating at: 17:49:05 rms-change max change #iterations 3.417844 158.5128 at 10iterations 1.392565 51.57541 at 20iterations 0.5673896 22.66856 at 30iterations 0.2326841 8.853263 at 40iterations 9.4341978E-02 3.505665 at 50iterations 3.8631465E-02 1.285049 at 60iterations 1.5793372E-02 0.5715256 at 70iterations 6.4922571E-03 0.2187462 at 80iterations 2.6748655E-03 8.8451385E-02 at 90iterations 1.1223205E-03 3.8425595E-02 at 100iterations 4.9089972E-04 1.7035484E-02 at 110iterations 2.2931020E-04 8.3312988E-03 at 120iterations finished qdiffx linear iterations at : 17:49:14 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 2.2931020E-04 8.3312988E-03 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 17:49:14 9.728u 0.315s 0:10.30 97.3% 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 17:49:14 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3531 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.362658 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): -0.8420000 44.60500 ymin,ymax (A): -30.65400 26.10800 zmin,zma (A): 1.427000 69.23200 x,y,z range (A): 45.44700 56.76200 67.80500 scale (grids/A): 2.362658 object centre (A): 21.88150 -2.273001 35.32950 number of atom coordinates read : 3531 total number of charged atoms : 3384 net assigned charge : -5.871982 assigned positive charge : 542.8039 centred at (gu) : 92.14791 98.27238 92.95189 assigned negative charge : -548.6779 centred at (gu) : 91.98102 98.07139 92.91875 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 162114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28899 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73876 mr = 119217 m= 19427 mr = 58680 m= 2697 mr = 14344 m= 144 mr = 1703 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 64264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 27023 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) : 1.575105 object centre at (A) : 21.88150 -2.273001 35.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1996932 7.3612243E-02 midg,1,midg; midg,igrid,midg -0.1130465 -0.1355101 1,midg,midg; igrid,midg,midg -7.6789536E-02 4.3379229E-02 gauss-seidel spectral radius is 0.9991103 estimated iterations to convergence 265 setup time was (sec) 1.880000 now iterating at: 17:49:16 rms-change max change #iterations 9.017934 246.5034 at 10iterations 4.993416 111.5599 at 20iterations 2.757164 60.33348 at 30iterations 1.512065 34.11409 at 40iterations 0.8302939 18.51481 at 50iterations 0.4523053 8.985667 at 60iterations 0.2475276 4.879285 at 70iterations 0.1350159 2.780401 at 80iterations 7.3599465E-02 1.530989 at 90iterations 4.0070727E-02 0.8714657 at 100iterations 2.1874381E-02 0.4579315 at 110iterations 1.1916894E-02 0.2363119 at 120iterations 6.5102451E-03 0.1289392 at 130iterations 3.5543786E-03 7.4505687E-02 at 140iterations 1.9541022E-03 3.8116455E-02 at 150iterations 1.0791637E-03 2.1835804E-02 at 160iterations 6.0598704E-04 1.2573361E-02 at 170iterations 3.4685180E-04 7.7767372E-03 at 180iterations finished qdiffx linear iterations at : 17:49:31 total time elapsed so far: 16.04000 # loops : 180 mean,max change (kT/e) : 3.4685180E-04 7.7767372E-03 energy calculations done at 16.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.23000 DelPhi exited at 17:49:31 16.232u 0.315s 0:16.82 98.3% 0+0k 0+0io 0pf+0w