Sat Oct 8 17:21:29 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 Sat Oct 8 2011 at 17:21:29 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 = 3495 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5326790 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): -3.104000 63.72800 ymin,ymax (A): 15.22600 76.27000 zmin,zma (A): -13.53500 34.21800 x,y,z range (A): 66.83200 61.04400 47.75300 scale (grids/A): 0.5326790 object centre (A): 30.31200 45.74800 10.34150 number of atom coordinates read : 3495 total number of charged atoms : 3349 net assigned charge : -4.999994 assigned positive charge : 526.7142 centred at (gu) : 89.41751 87.09216 89.62144 assigned negative charge : -531.7158 centred at (gu) : 89.42169 87.10194 89.64935 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6374 nv = 96 ne = 84 npr = 71147 no. pairs analyzed = 71147 no. exposed pairs = 4289 no. arc points = 29360 no. surface atoms = 1442 nbur = 2053 mkacc time = 0.1200000 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= 261 mr = 3424 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2400000 number of dielectric boundary points 3198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2945 ## 388 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8392 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6019217E-11 -2.8644476E-10 midg,1,midg; midg,igrid,midg -2.7956606E-10 -1.1263013E-10 1,midg,midg; igrid,midg,midg -1.8811233E-10 -1.7546903E-10 gauss-seidel spectral radius is 0.9818733 estimated iterations to convergence 61 setup time was (sec) 0.4400000 now iterating at: 17:21:30 rms-change max change #iterations 7.0464708E-02 12.47731 at 10iterations 4.4620461E-03 0.7952595 at 20iterations 3.2625953E-04 6.3203335E-02 at 30iterations 5.9120535E-05 1.5297890E-02 at 40iterations 1.7665965E-05 4.6749115E-03 at 50iterations finished qdiffx linear iterations at : 17:21:33 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 1.7665965E-05 4.6749115E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 17:21:33 3.683u 0.212s 0:04.17 93.2% 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 17:21:33 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 = 3495 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.598037 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): -3.104000 63.72800 ymin,ymax (A): 15.22600 76.27000 zmin,zma (A): -13.53500 34.21800 x,y,z range (A): 66.83200 61.04400 47.75300 scale (grids/A): 1.598037 object centre (A): 30.31200 45.74800 10.34150 number of atom coordinates read : 3495 total number of charged atoms : 3349 net assigned charge : -4.999994 assigned positive charge : 526.7142 centred at (gu) : 88.25161 81.27569 88.86343 assigned negative charge : -531.7158 centred at (gu) : 88.26480 81.30556 88.94749 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21968 mr = 49747 m= 2300 mr = 15088 m= 49 mr = 1125 m= 0 mr = 3 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 153 time to turn everything in is 0.3500000 number of dielectric boundary points 29698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 25450 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) : 0.5326790 object centre at (A) : 30.31200 45.74800 10.34150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0580403E-04 -1.0739678E-03 midg,1,midg; midg,igrid,midg -2.5367513E-02 -1.2068217E-02 1,midg,midg; igrid,midg,midg 1.2620408E-02 -4.6469797E-03 gauss-seidel spectral radius is 0.9981382 estimated iterations to convergence 184 setup time was (sec) 0.5700000 now iterating at: 17:21:34 rms-change max change #iterations 3.464690 153.8564 at 10iterations 1.425605 58.02625 at 20iterations 0.5877814 21.94476 at 30iterations 0.2433105 8.641301 at 40iterations 0.1004682 3.192947 at 50iterations 4.1584484E-02 1.620316 at 60iterations 1.7170601E-02 0.5956383 at 70iterations 7.1075917E-03 0.2239466 at 80iterations 2.9280940E-03 0.1000447 at 90iterations 1.2268332E-03 4.0864944E-02 at 100iterations 5.1071972E-04 1.7131805E-02 at 110iterations 2.1804811E-04 7.3375702E-03 at 120iterations finished qdiffx linear iterations at : 17:21:41 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 2.1804811E-04 7.3375702E-03 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 17:21:42 8.090u 0.243s 0:08.61 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 Sat Oct 8 2011 at 17:21:42 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 = 3495 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.397055 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): -3.104000 63.72800 ymin,ymax (A): 15.22600 76.27000 zmin,zma (A): -13.53500 34.21800 x,y,z range (A): 66.83200 61.04400 47.75300 scale (grids/A): 2.397055 object centre (A): 30.31200 45.74800 10.34150 number of atom coordinates read : 3495 total number of charged atoms : 3349 net assigned charge : -4.999994 assigned positive charge : 526.7142 centred at (gu) : 87.37704 76.91320 88.29458 assigned negative charge : -531.7158 centred at (gu) : 87.39724 76.95827 88.42107 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 166188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77363 mr = 121683 m= 21213 mr = 61629 m= 3490 mr = 15762 m= 228 mr = 2288 m= 1 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 485 time to turn everything in is 0.8800000 number of dielectric boundary points 67027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 26748 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) : 1.598037 object centre at (A) : 30.31200 45.74800 10.34150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4138639E-02 -1.3406684E-02 midg,1,midg; midg,igrid,midg -0.5045827 -0.1940412 1,midg,midg; igrid,midg,midg 0.4458236 -7.9700097E-02 gauss-seidel spectral radius is 0.9991244 estimated iterations to convergence 267 setup time was (sec) 1.130000 now iterating at: 17:21:43 rms-change max change #iterations 9.077597 319.8584 at 10iterations 5.075217 125.3771 at 20iterations 2.814879 63.80492 at 30iterations 1.562433 38.89690 at 40iterations 0.8601526 18.63400 at 50iterations 0.4750776 9.434454 at 60iterations 0.2609425 5.076187 at 70iterations 0.1431812 2.840904 at 80iterations 7.8649588E-02 1.617065 at 90iterations 4.3036953E-02 0.9095187 at 100iterations 2.3600524E-02 0.5229378 at 110iterations 1.2975808E-02 0.2715435 at 120iterations 7.0842332E-03 0.1357298 at 130iterations 3.8931423E-03 7.8212023E-02 at 140iterations 2.1349012E-03 4.3615341E-02 at 150iterations 1.1774749E-03 2.3109436E-02 at 160iterations 6.5242272E-04 1.2938499E-02 at 170iterations 3.6539123E-04 7.3604584E-03 at 180iterations finished qdiffx linear iterations at : 17:21:55 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 3.6539123E-04 7.3604584E-03 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 17:21:56 13.080u 0.228s 0:13.71 97.0% 0+0k 0+0io 0pf+0w