Sat Oct 8 14:00:52 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 14:00:52 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3005 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6384391 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): -12.26500 43.49600 ymin,ymax (A): -22.18600 22.69000 zmin,zma (A): -6.968000 46.53200 x,y,z range (A): 55.76100 44.87600 53.50000 scale (grids/A): 0.6384391 object centre (A): 15.61550 0.2519999 19.78200 number of atom coordinates read : 3005 total number of charged atoms : 2860 net assigned charge : 3.000005 assigned positive charge : 449.9537 centred at (gu) : 88.70918 89.44380 91.58662 assigned negative charge : -446.9544 centred at (gu) : 88.67228 89.29079 91.55513 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7890 nv = 96 ne = 84 npr = 64734 no. pairs analyzed = 64734 no. exposed pairs = 3334 no. arc points = 22947 no. surface atoms = 1137 nbur = 1868 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 4651 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2350 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9908 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2845999E-10 1.1691526E-08 midg,1,midg; midg,igrid,midg -1.7703439E-08 2.0903268E-08 1,midg,midg; igrid,midg,midg -6.8813494E-10 6.8494286E-09 gauss-seidel spectral radius is 0.9873129 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 14:00:53 rms-change max change #iterations 0.1579182 22.23921 at 10iterations 1.5680004E-02 1.928295 at 20iterations 1.5892652E-03 0.2190151 at 30iterations 1.5819527E-04 1.9001007E-02 at 40iterations 1.6532078E-05 2.1467209E-03 at 50iterations finished qdiffx linear iterations at : 14:00:55 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.6532078E-05 2.1467209E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:00:56 3.401u 0.176s 0:03.87 92.2% 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 14:00:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3005 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.915317 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): -12.26500 43.49600 ymin,ymax (A): -22.18600 22.69000 zmin,zma (A): -6.968000 46.53200 x,y,z range (A): 55.76100 44.87600 53.50000 scale (grids/A): 1.915317 object centre (A): 15.61550 0.2519999 19.78200 number of atom coordinates read : 3005 total number of charged atoms : 2860 net assigned charge : 3.000005 assigned positive charge : 449.9537 centred at (gu) : 86.12698 88.33086 94.75949 assigned negative charge : -446.9544 centred at (gu) : 86.01687 87.87215 94.66493 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22947 grid for indexing accessible points = 1.400000 m= 30345 mr = 63004 m= 4338 mr = 22817 m= 285 mr = 2689 m= 1 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 0.4200000 number of dielectric boundary points 32987 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22502 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) : 0.6384391 object centre at (A) : 15.61550 0.2519999 19.78200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3762300E-03 1.9856276E-02 midg,1,midg; midg,igrid,midg -4.2549833E-03 3.4167618E-02 1,midg,midg; igrid,midg,midg -2.7941717E-02 1.8740846E-02 gauss-seidel spectral radius is 0.9986730 estimated iterations to convergence 217 setup time was (sec) 0.6300000 now iterating at: 14:00:57 rms-change max change #iterations 4.641185 175.5884 at 10iterations 2.206283 65.96356 at 20iterations 1.042336 33.41777 at 30iterations 0.4949435 15.41738 at 40iterations 0.2349639 6.789080 at 50iterations 0.1112547 3.295803 at 60iterations 5.2777313E-02 1.594669 at 70iterations 2.5024651E-02 0.7998943 at 80iterations 1.1893438E-02 0.3463097 at 90iterations 5.6493045E-03 0.1604309 at 100iterations 2.6727752E-03 7.6265335E-02 at 110iterations 1.2736151E-03 3.6550522E-02 at 120iterations finished qdiffx linear iterations at : 14:01:04 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.2736151E-03 3.6550522E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:01:04 7.787u 0.200s 0:08.31 96.0% 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 Sat Oct 8 2011 at 14:01:04 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3005 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.872976 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): -12.26500 43.49600 ymin,ymax (A): -22.18600 22.69000 zmin,zma (A): -6.968000 46.53200 x,y,z range (A): 55.76100 44.87600 53.50000 scale (grids/A): 2.872976 object centre (A): 15.61550 0.2519999 19.78200 number of atom coordinates read : 3005 total number of charged atoms : 2860 net assigned charge : 3.000005 assigned positive charge : 449.9537 centred at (gu) : 84.19025 87.49626 97.13908 assigned negative charge : -446.9544 centred at (gu) : 84.02516 86.80814 96.99741 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 200993 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22947 grid for indexing accessible points = 1.400000 m= 100908 mr = 152158 m= 34244 mr = 84267 m= 7702 mr = 27687 m= 1152 mr = 5739 m= 87 mr = 828 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 521 time to turn everything in is 1.070000 number of dielectric boundary points 74367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 22880 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) : 1.915317 object centre at (A) : 15.61550 0.2519999 19.78200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0398658E-02 0.4132269 midg,1,midg; midg,igrid,midg -2.0375974E-02 0.3832541 1,midg,midg; igrid,midg,midg -0.4801616 0.2449442 gauss-seidel spectral radius is 0.9992687 estimated iterations to convergence 292 setup time was (sec) 1.310000 now iterating at: 14:01:06 rms-change max change #iterations 10.71372 422.3615 at 10iterations 6.247754 130.5212 at 20iterations 3.617592 67.75746 at 30iterations 2.095797 34.73629 at 40iterations 1.211467 24.02009 at 50iterations 0.6997271 16.31089 at 60iterations 0.4037750 6.793022 at 70iterations 0.2331910 3.948377 at 80iterations 0.1345461 2.217761 at 90iterations 7.7511214E-02 1.282840 at 100iterations 4.4677220E-02 0.7364140 at 110iterations 2.5789618E-02 0.4315071 at 120iterations 1.4867543E-02 0.2544479 at 130iterations 8.5826097E-03 0.1415863 at 140iterations 4.9478412E-03 9.0525627E-02 at 150iterations 2.8600285E-03 4.9279213E-02 at 160iterations 1.6593512E-03 2.7404785E-02 at 170iterations 9.5984450E-04 1.5436172E-02 at 180iterations finished qdiffx linear iterations at : 14:01:17 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 9.5984450E-04 1.5436172E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 14:01:17 12.699u 0.197s 0:13.17 97.7% 0+0k 0+0io 0pf+0w