Sun Oct 9 12:09:27 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 Sun Oct 9 2011 at 12:09:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 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: 0.6925800 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): -13.98000 37.42200 ymin,ymax (A): -1.061000 44.48200 zmin,zma (A): -6.372000 43.59900 x,y,z range (A): 51.40200 45.54300 49.97100 scale (grids/A): 0.6925800 object centre (A): 11.72100 21.71050 18.61350 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 372.5330 centred at (gu) : 91.07970 91.47961 89.76053 assigned negative charge : -368.0336 centred at (gu) : 91.23937 91.55471 89.71100 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7687 nv = 96 ne = 84 npr = 48915 no. pairs analyzed = 48915 no. exposed pairs = 3122 no. arc points = 21322 no. surface atoms = 1042 nbur = 1391 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 519 mr = 4268 m= 9 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1961 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8857 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5590707E-09 4.6073634E-08 midg,1,midg; midg,igrid,midg 4.3937082E-08 -5.3113745E-09 1,midg,midg; igrid,midg,midg 7.5002745E-08 -4.9497430E-08 gauss-seidel spectral radius is 0.9891701 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 12:09:28 rms-change max change #iterations 0.2021723 29.95045 at 10iterations 2.3938363E-02 3.665939 at 20iterations 2.9887487E-03 0.3767757 at 30iterations 4.6192561E-04 5.9715271E-02 at 40iterations 1.1104914E-04 1.3847351E-02 at 50iterations finished qdiffx linear iterations at : 12:09:31 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.1104914E-04 1.3847351E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 12:09:31 3.394u 0.162s 0:03.82 92.9% 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 Sun Oct 9 2011 at 12:09:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 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: 2.077740 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): -13.98000 37.42200 ymin,ymax (A): -1.061000 44.48200 zmin,zma (A): -6.372000 43.59900 x,y,z range (A): 51.40200 45.54300 49.97100 scale (grids/A): 2.077740 object centre (A): 11.72100 21.71050 18.61350 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 372.5330 centred at (gu) : 93.23853 94.43849 89.28080 assigned negative charge : -368.0336 centred at (gu) : 93.71803 94.66397 89.13275 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 81208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21322 grid for indexing accessible points = 1.400000 m= 32018 mr = 56110 m= 6216 mr = 23877 m= 548 mr = 4049 m= 9 mr = 267 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 35694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 18189 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) : 0.6925800 object centre at (A) : 11.72100 21.71050 18.61350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8117634E-02 1.8185133E-02 midg,1,midg; midg,igrid,midg 2.9821206E-02 7.6422705E-03 1,midg,midg; igrid,midg,midg 2.8671855E-02 -3.9323628E-02 gauss-seidel spectral radius is 0.9988231 estimated iterations to convergence 231 setup time was (sec) 0.6500000 now iterating at: 12:09:32 rms-change max change #iterations 4.880973 187.2189 at 10iterations 2.392749 85.55946 at 20iterations 1.184621 38.25306 at 30iterations 0.5879819 17.83958 at 40iterations 0.2905101 8.776846 at 50iterations 0.1434847 4.578857 at 60iterations 7.1144670E-02 2.012276 at 70iterations 3.5189722E-02 1.009174 at 80iterations 1.7553303E-02 0.5005970 at 90iterations 8.6984448E-03 0.2765656 at 100iterations 4.3372884E-03 0.1310143 at 110iterations 2.1938914E-03 7.0255280E-02 at 120iterations finished qdiffx linear iterations at : 12:09:39 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.1938914E-03 7.0255280E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 12:09:40 7.972u 0.187s 0:08.42 96.7% 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 Sun Oct 9 2011 at 12:09:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 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: 3.116610 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): -13.98000 37.42200 ymin,ymax (A): -1.061000 44.48200 zmin,zma (A): -6.372000 43.59900 x,y,z range (A): 51.40200 45.54300 49.97100 scale (grids/A): 3.116610 object centre (A): 11.72100 21.71050 18.61350 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 372.5330 centred at (gu) : 94.85768 96.65753 88.92116 assigned negative charge : -368.0336 centred at (gu) : 95.57710 96.99590 88.69913 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 186660 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21322 grid for indexing accessible points = 1.400000 m= 99100 mr = 135051 m= 40776 mr = 81133 m= 11778 mr = 33349 m= 2282 mr = 9016 m= 209 mr = 1632 m= 6 mr = 103 m= 0 mr = 2 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 80525 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 18328 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) : 2.077740 object centre at (A) : 11.72100 21.71050 18.61350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2498602 6.8322055E-02 midg,1,midg; midg,igrid,midg 0.2377335 -8.4026255E-02 1,midg,midg; igrid,midg,midg 0.4852850 -0.4096412 gauss-seidel spectral radius is 0.9992989 estimated iterations to convergence 298 setup time was (sec) 1.500000 now iterating at: 12:09:42 rms-change max change #iterations 11.05617 382.4601 at 10iterations 6.562303 147.0560 at 20iterations 3.888872 75.04971 at 30iterations 2.299300 59.00127 at 40iterations 1.359204 27.67761 at 50iterations 0.7999084 14.06125 at 60iterations 0.4702623 8.868042 at 70iterations 0.2753752 4.530556 at 80iterations 0.1617747 2.719284 at 90iterations 9.4692580E-02 1.810135 at 100iterations 5.5554394E-02 0.9571457 at 110iterations 3.2561090E-02 0.5509443 at 120iterations 1.9165492E-02 0.3266468 at 130iterations 1.1274351E-02 0.1883469 at 140iterations 6.6846893E-03 0.1149368 at 150iterations 4.0062866E-03 7.5328827E-02 at 160iterations 2.4422621E-03 4.9266815E-02 at 170iterations 1.5356528E-03 3.1850815E-02 at 180iterations finished qdiffx linear iterations at : 12:09:53 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 1.5356528E-03 3.1850815E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 12:09:53 12.872u 0.214s 0:13.35 97.9% 0+0k 0+0io 0pf+0w