Mon Oct 10 10:41:22 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 Mon Oct 10 2011 at 10:41:22 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5406473 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): 3.751000 62.98700 ymin,ymax (A): -24.19900 37.85400 zmin,zma (A): -33.44000 32.40700 x,y,z range (A): 59.23600 62.05300 65.84700 scale (grids/A): 0.5406473 object centre (A): 33.36900 6.827500 -0.5165024 number of atom coordinates read : 5014 total number of charged atoms : 4814 net assigned charge : 8.500036 assigned positive charge : 779.4674 centred at (gu) : 89.76960 90.85537 88.64524 assigned negative charge : -770.9746 centred at (gu) : 89.79698 90.89323 88.64337 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9438 nv = 96 ne = 84 npr = 100668 no. pairs analyzed = 100668 no. exposed pairs = 5767 no. arc points = 38715 no. surface atoms = 1934 nbur = 3080 mkacc time = 0.2700000 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 = 1.596000 m= 363 mr = 5452 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 145 time to turn everything in is 0.5200000 number of dielectric boundary points 4338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3953 ## 519 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 12417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7431765E-10 3.2311454E-10 midg,1,midg; midg,igrid,midg 6.3526695E-10 8.5241730E-11 1,midg,midg; igrid,midg,midg 7.2691192E-10 1.6341434E-10 gauss-seidel spectral radius is 0.9825084 estimated iterations to convergence 62 setup time was (sec) 0.8500000 now iterating at: 10:41:23 rms-change max change #iterations 9.5966488E-02 11.82342 at 10iterations 6.5303482E-03 0.8478584 at 20iterations 7.4543955E-04 0.1019993 at 30iterations 3.1314194E-04 4.2156696E-02 at 40iterations 1.6057797E-04 2.1668434E-02 at 50iterations finished qdiffx linear iterations at : 10:41:27 total time elapsed so far: 4.540000 # loops : 50 mean,max change (kT/e) : 1.6057797E-04 2.1668434E-02 energy calculations done at 4.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.710000 DelPhi exited at 10:41:27 4.713u 0.385s 0:05.47 93.0% 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 Mon Oct 10 2011 at 10:41:27 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.621942 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): 3.751000 62.98700 ymin,ymax (A): -24.19900 37.85400 zmin,zma (A): -33.44000 32.40700 x,y,z range (A): 59.23600 62.05300 65.84700 scale (grids/A): 1.621942 object centre (A): 33.36900 6.827500 -0.5165024 number of atom coordinates read : 5014 total number of charged atoms : 4814 net assigned charge : 8.500036 assigned positive charge : 779.4674 centred at (gu) : 89.30658 92.56409 85.93401 assigned negative charge : -770.9746 centred at (gu) : 89.39095 92.67959 85.93029 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 107446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38715 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 35226 mr = 78536 m= 3570 mr = 25632 m= 93 mr = 1821 m= 0 mr = 7 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5535 time to turn everything in is 0.8500000 number of dielectric boundary points 40339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 409 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 36729 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) : 0.5406473 object centre at (A) : 33.36900 6.827500 -0.5165024 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5547620E-02 6.3537783E-03 midg,1,midg; midg,igrid,midg 2.4929382E-02 1.1433275E-02 1,midg,midg; igrid,midg,midg -3.3728920E-03 -5.8296816E-03 gauss-seidel spectral radius is 0.9983501 estimated iterations to convergence 195 setup time was (sec) 1.150000 now iterating at: 10:41:29 rms-change max change #iterations 4.524986 158.0081 at 10iterations 1.959931 57.76510 at 20iterations 0.8553135 27.04136 at 30iterations 0.3732152 10.49019 at 40iterations 0.1625383 4.762802 at 50iterations 7.0810080E-02 1.971557 at 60iterations 3.0882511E-02 0.8994007 at 70iterations 1.3532019E-02 0.3865852 at 80iterations 5.9796418E-03 0.1654015 at 90iterations 2.7308126E-03 7.7387810E-02 at 100iterations 1.3478176E-03 4.2793274E-02 at 110iterations 7.7526050E-04 2.5009155E-02 at 120iterations finished qdiffx linear iterations at : 10:41:39 total time elapsed so far: 10.75000 # loops : 120 mean,max change (kT/e) : 7.7526050E-04 2.5009155E-02 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.91000 DelPhi exited at 10:41:39 10.916u 0.460s 0:11.67 97.4% 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 Mon Oct 10 2011 at 10:41:39 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.432913 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): 3.751000 62.98700 ymin,ymax (A): -24.19900 37.85400 zmin,zma (A): -33.44000 32.40700 x,y,z range (A): 59.23600 62.05300 65.84700 scale (grids/A): 2.432913 object centre (A): 33.36900 6.827500 -0.5165024 number of atom coordinates read : 5014 total number of charged atoms : 4814 net assigned charge : 8.500036 assigned positive charge : 779.4674 centred at (gu) : 88.95950 93.84566 83.90070 assigned negative charge : -770.9746 centred at (gu) : 89.08632 94.01939 83.89548 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 250197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38715 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 122568 mr = 191136 m= 35365 mr = 100534 m= 5573 mr = 27399 m= 340 mr = 3750 m= 7 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 18492 time to turn everything in is 2.120000 number of dielectric boundary points 91077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 38457 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) : 1.621942 object centre at (A) : 33.36900 6.827500 -0.5165024 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4916919 7.2462700E-02 midg,1,midg; midg,igrid,midg 0.5287836 9.7856529E-02 1,midg,midg; igrid,midg,midg -0.1014502 7.3705199E-03 gauss-seidel spectral radius is 0.9992214 estimated iterations to convergence 283 setup time was (sec) 2.470000 now iterating at: 10:41:42 rms-change max change #iterations 11.54341 266.1931 at 10iterations 6.680278 141.6147 at 20iterations 3.855063 87.87614 at 30iterations 2.215678 47.94893 at 40iterations 1.270057 23.52716 at 50iterations 0.7248812 13.56670 at 60iterations 0.4144050 6.834658 at 70iterations 0.2357187 3.878478 at 80iterations 0.1341696 2.395409 at 90iterations 7.6352939E-02 1.285862 at 100iterations 4.3462202E-02 0.7455139 at 110iterations 2.4685126E-02 0.4259796 at 120iterations 1.4008387E-02 0.2418375 at 130iterations 7.9588993E-03 0.1350975 at 140iterations 4.5127464E-03 7.9526901E-02 at 150iterations 2.5621646E-03 4.4333458E-02 at 160iterations 1.4564403E-03 2.5804520E-02 at 170iterations 8.2683598E-04 1.4845848E-02 at 180iterations finished qdiffx linear iterations at : 10:42:00 total time elapsed so far: 20.64000 # loops : 180 mean,max change (kT/e) : 8.2683598E-04 1.4845848E-02 energy calculations done at 20.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.81000 DelPhi exited at 10:42:01 20.815u 0.497s 0:21.57 98.7% 0+0k 0+0io 0pf+0w