Sun Oct 9 19:12:38 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 19:12:38 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4866 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5591857 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): 3.436000 64.58600 ymin,ymax (A): -8.897000 52.37600 zmin,zma (A): -2.150000 61.51400 x,y,z range (A): 61.15000 61.27300 63.66400 scale (grids/A): 0.5591857 object centre (A): 34.01100 21.73950 29.68200 number of atom coordinates read : 4866 total number of charged atoms : 4693 net assigned charge : 2.740032 assigned positive charge : 738.6848 centred at (gu) : 88.25632 89.53659 89.43705 assigned negative charge : -735.9498 centred at (gu) : 88.11756 89.56824 89.38878 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10022 nv = 96 ne = 84 npr = 98802 no. pairs analyzed = 98802 no. exposed pairs = 5687 no. arc points = 38415 no. surface atoms = 1952 nbur = 2914 mkacc time = 0.1600000 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 = 1.540000 m= 477 mr = 5788 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3963 ## 474 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13055 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0814087E-10 1.0337798E-09 midg,1,midg; midg,igrid,midg 9.9996622E-10 -2.0350294E-10 1,midg,midg; igrid,midg,midg -3.3604703E-09 1.8042375E-09 gauss-seidel spectral radius is 0.9836441 estimated iterations to convergence 64 setup time was (sec) 0.5300000 now iterating at: 19:12:39 rms-change max change #iterations 0.1126409 14.06546 at 10iterations 1.6119340E-02 2.054863 at 20iterations 6.6987779E-03 0.9385757 at 30iterations 3.2148755E-03 0.4513550 at 40iterations 1.5597395E-03 0.2164383 at 50iterations finished qdiffx linear iterations at : 19:12:42 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.5597395E-03 0.2164383 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 19:12:42 3.560u 0.194s 0:04.03 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 Sun Oct 9 2011 at 19:12:43 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4866 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.677557 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): 3.436000 64.58600 ymin,ymax (A): -8.897000 52.37600 zmin,zma (A): -2.150000 61.51400 x,y,z range (A): 61.15000 61.27300 63.66400 scale (grids/A): 1.677557 object centre (A): 34.01100 21.73950 29.68200 number of atom coordinates read : 4866 total number of charged atoms : 4693 net assigned charge : 2.740032 assigned positive charge : 738.6848 centred at (gu) : 84.76789 88.60840 88.30987 assigned negative charge : -735.9498 centred at (gu) : 84.35250 88.70463 88.16611 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 112117 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38415 grid for indexing accessible points = 1.400000 m= 39297 mr = 81496 m= 4947 mr = 28586 m= 181 mr = 2703 m= 3 mr = 27 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 0.5400000 number of dielectric boundary points 43733 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 0.6300000 number of grid points assigned charge 36222 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) : 0.5591857 object centre at (A) : 34.01100 21.73950 29.68200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8579774E-02 -2.1790287E-03 midg,1,midg; midg,igrid,midg 1.3780083E-02 1.1039669E-02 1,midg,midg; igrid,midg,midg -1.5909674E-02 3.7472945E-02 gauss-seidel spectral radius is 0.9984615 estimated iterations to convergence 202 setup time was (sec) 0.7700000 now iterating at: 19:12:43 rms-change max change #iterations 4.736513 179.0916 at 10iterations 2.120227 66.35736 at 20iterations 0.9482629 28.04331 at 30iterations 0.4268533 11.31569 at 40iterations 0.1928287 5.277596 at 50iterations 8.8428207E-02 2.686735 at 60iterations 4.2472955E-02 1.286285 at 70iterations 2.2297604E-02 0.7273865 at 80iterations 1.3215072E-02 0.4102812 at 90iterations 9.0098288E-03 0.2713776 at 100iterations 6.6010798E-03 0.1928177 at 110iterations 4.9950848E-03 0.1422348 at 120iterations finished qdiffx linear iterations at : 19:12:51 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 4.9950848E-03 0.1422348 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 19:12:51 8.216u 0.194s 0:08.85 94.9% 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 19:12:51 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4866 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.516336 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): 3.436000 64.58600 ymin,ymax (A): -8.897000 52.37600 zmin,zma (A): -2.150000 61.51400 x,y,z range (A): 61.15000 61.27300 63.66400 scale (grids/A): 2.516336 object centre (A): 34.01100 21.73950 29.68200 number of atom coordinates read : 4866 total number of charged atoms : 4693 net assigned charge : 2.740032 assigned positive charge : 738.6848 centred at (gu) : 82.15147 87.91225 87.46461 assigned negative charge : -735.9498 centred at (gu) : 81.52882 88.05686 87.24931 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 260697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38415 grid for indexing accessible points = 1.400000 m= 132364 mr = 198314 m= 42330 mr = 108348 m= 8117 mr = 32996 m= 741 mr = 5586 m= 14 mr = 432 m= 0 mr = 2 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 98585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 37496 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) : 1.677557 object centre at (A) : 34.01100 21.73950 29.68200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3446784 6.8515532E-02 midg,1,midg; midg,igrid,midg -1.1220835E-02 -1.6474223E-02 1,midg,midg; igrid,midg,midg -0.3343195 0.6031777 gauss-seidel spectral radius is 0.9992583 estimated iterations to convergence 290 setup time was (sec) 1.620000 now iterating at: 19:12:53 rms-change max change #iterations 12.05012 301.1905 at 10iterations 7.129344 137.1237 at 20iterations 4.184769 83.05727 at 30iterations 2.447060 41.77802 at 40iterations 1.428336 27.59430 at 50iterations 0.8291292 13.42559 at 60iterations 0.4808650 8.137131 at 70iterations 0.2789654 4.684006 at 80iterations 0.1617277 2.643345 at 90iterations 9.4000347E-02 1.600452 at 100iterations 5.5255331E-02 0.9622765 at 110iterations 3.3068810E-02 0.5370636 at 120iterations 2.0435667E-02 0.3890381 at 130iterations 1.3371750E-02 0.2576218 at 140iterations 9.3927672E-03 0.1736183 at 150iterations 7.0883771E-03 0.1241684 at 160iterations 5.6483024E-03 9.7476959E-02 at 170iterations 4.6417057E-03 7.7903748E-02 at 180iterations finished qdiffx linear iterations at : 19:13:05 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 4.6417057E-03 7.7903748E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 19:13:05 13.592u 0.203s 0:14.06 98.0% 0+0k 0+0io 0pf+0w