Mon Oct 10 22:01:37 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 22:01:37 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 = 2430 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6557256 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): 2.699000 54.32900 ymin,ymax (A): -21.44200 32.84900 zmin,zma (A): 7.618001 49.89200 x,y,z range (A): 51.63000 54.29100 42.27400 scale (grids/A): 0.6557256 object centre (A): 28.51400 5.703500 28.75500 number of atom coordinates read : 2430 total number of charged atoms : 2295 net assigned charge : 7.000006 assigned positive charge : 354.2590 centred at (gu) : 91.78714 91.65829 89.75610 assigned negative charge : -347.2600 centred at (gu) : 91.84380 91.60577 89.68703 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7069 nv = 96 ne = 84 npr = 49535 no. pairs analyzed = 49535 no. exposed pairs = 3167 no. arc points = 22008 no. surface atoms = 1069 nbur = 1361 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3761 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2107 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8307 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0533884E-09 2.5297464E-08 midg,1,midg; midg,igrid,midg 5.4857199E-09 3.3924589E-08 1,midg,midg; igrid,midg,midg 1.7142540E-08 9.5404467E-09 gauss-seidel spectral radius is 0.9879367 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 22:01:37 rms-change max change #iterations 0.1490789 22.51055 at 10iterations 1.5890613E-02 2.193059 at 20iterations 1.7280739E-03 0.2273102 at 30iterations 2.4931959E-04 3.4564018E-02 at 40iterations 5.5825934E-05 5.9890747E-03 at 50iterations finished qdiffx linear iterations at : 22:01:40 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 5.5825934E-05 5.9890747E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 22:01:41 3.299u 0.171s 0:04.11 84.1% 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 22:01:41 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 = 2430 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.967177 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): 2.699000 54.32900 ymin,ymax (A): -21.44200 32.84900 zmin,zma (A): 7.618001 49.89200 x,y,z range (A): 51.63000 54.29100 42.27400 scale (grids/A): 1.967177 object centre (A): 28.51400 5.703500 28.75500 number of atom coordinates read : 2430 total number of charged atoms : 2295 net assigned charge : 7.000006 assigned positive charge : 354.2590 centred at (gu) : 95.36112 94.97427 89.26786 assigned negative charge : -347.2600 centred at (gu) : 95.53133 94.81723 89.06096 start vw surface at 0.2300000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 76271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22008 grid for indexing accessible points = 1.400000 m= 27222 mr = 52044 m= 4519 mr = 19538 m= 270 mr = 2916 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 211 time to turn everything in is 0.6300000 number of dielectric boundary points 33676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18146 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) : 0.6557256 object centre at (A) : 28.51400 5.703500 28.75500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1655305E-02 3.2423172E-02 midg,1,midg; midg,igrid,midg 2.2649348E-03 1.9144444E-02 1,midg,midg; igrid,midg,midg -4.6221362E-03 1.3198584E-02 gauss-seidel spectral radius is 0.9987086 estimated iterations to convergence 220 setup time was (sec) 0.9000000 now iterating at: 22:01:42 rms-change max change #iterations 4.232721 202.2373 at 10iterations 2.022517 76.19089 at 20iterations 0.9640785 31.08481 at 30iterations 0.4613198 16.77627 at 40iterations 0.2198185 6.811329 at 50iterations 0.1056420 3.224998 at 60iterations 5.0393779E-02 1.763519 at 70iterations 2.4125012E-02 0.7818012 at 80iterations 1.1559939E-02 0.3481445 at 90iterations 5.5516888E-03 0.1708422 at 100iterations 2.6722683E-03 8.2272053E-02 at 110iterations 1.2919371E-03 4.3366909E-02 at 120iterations finished qdiffx linear iterations at : 22:01:50 total time elapsed so far: 8.810000 # loops : 120 mean,max change (kT/e) : 1.2919371E-03 4.3366909E-02 energy calculations done at 8.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.980000 DelPhi exited at 22:01:50 8.978u 0.235s 0:09.62 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 Mon Oct 10 2011 at 22:01:50 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 = 2430 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.950765 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): 2.699000 54.32900 ymin,ymax (A): -21.44200 32.84900 zmin,zma (A): 7.618001 49.89200 x,y,z range (A): 51.63000 54.29100 42.27400 scale (grids/A): 2.950765 object centre (A): 28.51400 5.703500 28.75500 number of atom coordinates read : 2430 total number of charged atoms : 2295 net assigned charge : 7.000006 assigned positive charge : 354.2590 centred at (gu) : 98.04157 97.46129 88.90181 assigned negative charge : -347.2600 centred at (gu) : 98.29720 97.22586 88.59134 start vw surface at 0.2000000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 176343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22008 grid for indexing accessible points = 1.400000 m= 87152 mr = 126440 m= 32114 mr = 69846 m= 8200 mr = 25605 m= 1147 mr = 6290 m= 99 mr = 773 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 629 time to turn everything in is 1.390000 number of dielectric boundary points 76040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 18360 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) : 1.967177 object centre at (A) : 28.51400 5.703500 28.75500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0773691E-02 0.3071536 midg,1,midg; midg,igrid,midg 8.1853718E-02 0.1236202 1,midg,midg; igrid,midg,midg -8.9613885E-02 8.1413217E-02 gauss-seidel spectral radius is 0.9992876 estimated iterations to convergence 296 setup time was (sec) 1.660000 now iterating at: 22:01:52 rms-change max change #iterations 10.06860 424.6417 at 10iterations 6.005915 120.2658 at 20iterations 3.574750 80.96806 at 30iterations 2.115930 41.84680 at 40iterations 1.248256 21.78418 at 50iterations 0.7350323 16.28554 at 60iterations 0.4302765 8.823922 at 70iterations 0.2519780 4.831978 at 80iterations 0.1476362 2.665183 at 90iterations 8.6085960E-02 1.597943 at 100iterations 5.0338801E-02 0.8866081 at 110iterations 2.9428979E-02 0.5465708 at 120iterations 1.7132385E-02 0.3021240 at 130iterations 1.0005448E-02 0.1777925 at 140iterations 5.8621992E-03 0.1053917 at 150iterations 3.4269993E-03 5.8546066E-02 at 160iterations 2.0157753E-03 3.7820816E-02 at 170iterations 1.1980641E-03 2.2541046E-02 at 180iterations finished qdiffx linear iterations at : 22:02:02 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 1.1980641E-03 2.2541046E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 22:02:02 11.449u 0.169s 0:11.90 97.4% 0+0k 0+0io 0pf+0w