Sat Oct 15 13:18:20 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 Sat Oct 15 2011 at 13:18:20 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! 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: 0.5739344 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): -11.22200 50.80600 ymin,ymax (A): -12.70900 42.48800 zmin,zma (A): 17.67300 75.60201 x,y,z range (A): 62.02800 55.19700 57.92900 scale (grids/A): 0.5739344 object centre (A): 19.79200 14.88950 46.63750 number of atom coordinates read : 3363 total number of charged atoms : 3217 net assigned charge : 3.240019 assigned positive charge : 522.8699 centred at (gu) : 90.83274 89.81852 88.25694 assigned negative charge : -519.6310 centred at (gu) : 90.76624 89.90305 88.23485 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7471 nv = 96 ne = 84 npr = 65140 no. pairs analyzed = 65140 no. exposed pairs = 4522 no. arc points = 32130 no. surface atoms = 1524 nbur = 1839 mkacc time = 0.1800000 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 = 1.484000 m= 360 mr = 3710 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3163 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9314 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3490081E-10 6.8385192E-10 midg,1,midg; midg,igrid,midg 2.4159521E-09 -1.1696312E-09 1,midg,midg; igrid,midg,midg -6.8254613E-10 2.3701239E-09 gauss-seidel spectral radius is 0.9843714 estimated iterations to convergence 66 setup time was (sec) 0.7500000 now iterating at: 13:18:21 rms-change max change #iterations 9.8556407E-02 13.81056 at 10iterations 7.4373432E-03 1.330476 at 20iterations 5.7143805E-04 9.2170715E-02 at 30iterations 4.7610494E-05 6.8130493E-03 at 40iterations 1.1236061E-05 1.6137362E-03 at 50iterations finished qdiffx linear iterations at : 13:18:25 total time elapsed so far: 5.200000 # loops : 50 mean,max change (kT/e) : 1.1236061E-05 1.6137362E-03 energy calculations done at 5.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.370000 DelPhi exited at 13:18:26 5.372u 0.428s 0:06.27 92.3% 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 15 2011 at 13:18:26 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! 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: 1.721803 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): -11.22200 50.80600 ymin,ymax (A): -12.70900 42.48800 zmin,zma (A): 17.67300 75.60201 x,y,z range (A): 62.02800 55.19700 57.92900 scale (grids/A): 1.721803 object centre (A): 19.79200 14.88950 46.63750 number of atom coordinates read : 3363 total number of charged atoms : 3217 net assigned charge : 3.240019 assigned positive charge : 522.8699 centred at (gu) : 92.49726 89.45470 84.76955 assigned negative charge : -519.6310 centred at (gu) : 92.29820 89.70895 84.70427 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32130 grid for indexing accessible points = 1.400000 m= 27144 mr = 54545 m= 3457 mr = 18119 m= 137 mr = 1774 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 37681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 24933 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) : 0.5739344 object centre at (A) : 19.79200 14.88950 46.63750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8694112E-03 7.5757764E-03 midg,1,midg; midg,igrid,midg 2.2109024E-02 -9.2858076E-03 1,midg,midg; igrid,midg,midg -1.2696574E-02 -8.0070253E-03 gauss-seidel spectral radius is 0.9984202 estimated iterations to convergence 200 setup time was (sec) 1.060000 now iterating at: 13:18:28 rms-change max change #iterations 4.147228 154.8129 at 10iterations 1.830241 63.34734 at 20iterations 0.8125294 29.31489 at 30iterations 0.3595744 12.96301 at 40iterations 0.1590171 4.925444 at 50iterations 7.0824049E-02 2.375561 at 60iterations 3.1445157E-02 1.019935 at 70iterations 1.3981460E-02 0.5189056 at 80iterations 6.2225419E-03 0.2339554 at 90iterations 2.8054731E-03 9.8419189E-02 at 100iterations 1.3063014E-03 5.2650452E-02 at 110iterations 6.6444173E-04 2.4015427E-02 at 120iterations finished qdiffx linear iterations at : 13:18:41 total time elapsed so far: 13.22000 # loops : 120 mean,max change (kT/e) : 6.6444173E-04 2.4015427E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 13:18:41 13.392u 0.535s 0:15.04 92.5% 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 15 2011 at 13:18:41 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! 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: 2.582705 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): -11.22200 50.80600 ymin,ymax (A): -12.70900 42.48800 zmin,zma (A): 17.67300 75.60201 x,y,z range (A): 62.02800 55.19700 57.92900 scale (grids/A): 2.582705 object centre (A): 19.79200 14.88950 46.63750 number of atom coordinates read : 3363 total number of charged atoms : 3217 net assigned charge : 3.240019 assigned positive charge : 522.8699 centred at (gu) : 93.74588 89.18193 82.15417 assigned negative charge : -519.6310 centred at (gu) : 93.44721 89.56336 82.05639 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 188623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32130 grid for indexing accessible points = 1.400000 m= 90001 mr = 133302 m= 28819 mr = 70241 m= 5842 mr = 21141 m= 600 mr = 3871 m= 18 mr = 301 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.790000 number of dielectric boundary points 85047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 25715 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) : 1.721803 object centre at (A) : 19.79200 14.88950 46.63750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0627737E-02 8.9733079E-02 midg,1,midg; midg,igrid,midg 0.3603242 -0.1051280 1,midg,midg; igrid,midg,midg 1.9851523E-02 -0.5532197 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 2.210000 now iterating at: 13:18:44 rms-change max change #iterations 10.58229 290.4467 at 10iterations 6.264085 153.6190 at 20iterations 3.654062 85.14558 at 30iterations 2.115665 49.53122 at 40iterations 1.223550 31.35773 at 50iterations 0.7030432 15.72724 at 60iterations 0.4030406 9.633580 at 70iterations 0.2304519 4.688666 at 80iterations 0.1316554 2.539557 at 90iterations 7.5336330E-02 1.529278 at 100iterations 4.2979117E-02 0.8187084 at 110iterations 2.4479119E-02 0.4866714 at 120iterations 1.3938924E-02 0.2779117 at 130iterations 7.9559237E-03 0.1706867 at 140iterations 4.5462102E-03 8.8321686E-02 at 150iterations 2.6022561E-03 5.0031662E-02 at 160iterations 1.5037607E-03 2.8228641E-02 at 170iterations 8.9313323E-04 1.9088745E-02 at 180iterations finished qdiffx linear iterations at : 13:19:15 total time elapsed so far: 22.26000 # loops : 180 mean,max change (kT/e) : 8.9313323E-04 1.9088745E-02 energy calculations done at 22.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.43000 DelPhi exited at 13:19:16 22.436u 0.534s 0:34.34 66.8% 0+0k 0+0io 0pf+0w