Mon Oct 10 14:39:24 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 Mon Oct 10 2011 at 14:39:24 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 0.6255381 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): -7.483000 44.00500 ymin,ymax (A): 13.00300 69.91400 zmin,zma (A): 55.68000 107.4880 x,y,z range (A): 51.48800 56.91100 51.80800 scale (grids/A): 0.6255381 object centre (A): 18.26100 41.45850 81.58400 number of atom coordinates read : 2449 total number of charged atoms : 2290 net assigned charge : -3.999989 assigned positive charge : 362.3820 centred at (gu) : 89.88864 90.83673 89.93287 assigned negative charge : -366.3824 centred at (gu) : 89.65124 90.79079 89.90934 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6493 nv = 96 ne = 84 npr = 48931 no. pairs analyzed = 48931 no. exposed pairs = 3353 no. arc points = 23575 no. surface atoms = 1126 nbur = 1323 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3302 m= 0 mr = 17 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2233 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6079497E-09 -2.0373832E-09 midg,1,midg; midg,igrid,midg -6.0030074E-09 -4.7218884E-10 1,midg,midg; igrid,midg,midg -2.2272648E-08 1.2894669E-08 gauss-seidel spectral radius is 0.9867585 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 14:39:25 rms-change max change #iterations 0.1286472 19.83408 at 10iterations 1.1896938E-02 1.896725 at 20iterations 1.1248470E-03 0.1846390 at 30iterations 1.0461464E-04 1.5718460E-02 at 40iterations 9.8642049E-06 1.4553070E-03 at 50iterations finished qdiffx linear iterations at : 14:39:28 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 9.8642049E-06 1.4553070E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 14:39:29 4.077u 0.255s 0:05.02 86.0% 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 Mon Oct 10 2011 at 14:39:29 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 1.876614 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): -7.483000 44.00500 ymin,ymax (A): 13.00300 69.91400 zmin,zma (A): 55.68000 107.4880 x,y,z range (A): 51.48800 56.91100 51.80800 scale (grids/A): 1.876614 object centre (A): 18.26100 41.45850 81.58400 number of atom coordinates read : 2449 total number of charged atoms : 2290 net assigned charge : -3.999989 assigned positive charge : 362.3820 centred at (gu) : 89.66541 92.50960 89.79818 assigned negative charge : -366.3824 centred at (gu) : 88.95349 92.37198 89.72765 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23575 grid for indexing accessible points = 1.400000 m= 23290 mr = 46412 m= 3120 mr = 16153 m= 153 mr = 1552 m= 0 mr = 33 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 32290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17998 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) : 0.6255381 object centre at (A) : 18.26100 41.45850 81.58400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8895559E-02 2.6212640E-03 midg,1,midg; midg,igrid,midg -3.6758000E-03 -6.0817478E-03 1,midg,midg; igrid,midg,midg -4.1287482E-02 5.2803676E-03 gauss-seidel spectral radius is 0.9985873 estimated iterations to convergence 211 setup time was (sec) 0.9200000 now iterating at: 14:39:30 rms-change max change #iterations 3.994305 204.2293 at 10iterations 1.847961 68.25854 at 20iterations 0.8501817 31.29317 at 30iterations 0.3928483 12.57790 at 40iterations 0.1804899 6.603167 at 50iterations 8.3236642E-02 3.048650 at 60iterations 3.8290694E-02 1.264275 at 70iterations 1.7759161E-02 0.7010517 at 80iterations 8.1584919E-03 0.2535553 at 90iterations 3.7729698E-03 0.1318760 at 100iterations 1.7427726E-03 5.7861328E-02 at 110iterations 8.0356275E-04 2.9905021E-02 at 120iterations finished qdiffx linear iterations at : 14:39:39 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 8.0356275E-04 2.9905021E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 14:39:39 9.390u 0.302s 0:10.10 95.9% 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 Mon Oct 10 2011 at 14:39:39 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 2.814921 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): -7.483000 44.00500 ymin,ymax (A): 13.00300 69.91400 zmin,zma (A): 55.68000 107.4880 x,y,z range (A): 51.48800 56.91100 51.80800 scale (grids/A): 2.814921 object centre (A): 18.26100 41.45850 81.58400 number of atom coordinates read : 2449 total number of charged atoms : 2290 net assigned charge : -3.999989 assigned positive charge : 362.3820 centred at (gu) : 89.49818 93.76423 89.69719 assigned negative charge : -366.3824 centred at (gu) : 88.43005 93.55798 89.59132 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 161541 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23575 grid for indexing accessible points = 1.400000 m= 77314 mr = 113267 m= 25531 mr = 61237 m= 5095 mr = 19196 m= 570 mr = 3331 m= 31 mr = 269 m= 0 mr = 14 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 72768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 18320 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) : 1.876614 object centre at (A) : 18.26100 41.45850 81.58400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3123902 3.7568953E-02 midg,1,midg; midg,igrid,midg -3.7127037E-02 -0.1101264 1,midg,midg; igrid,midg,midg -0.4300659 -8.4668603E-03 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 1.920000 now iterating at: 14:39:42 rms-change max change #iterations 9.589101 383.3859 at 10iterations 5.655334 133.6918 at 20iterations 3.292320 76.60150 at 30iterations 1.911157 40.19736 at 40iterations 1.105327 24.28487 at 50iterations 0.6394735 12.86707 at 60iterations 0.3677916 7.794281 at 70iterations 0.2119356 4.207090 at 80iterations 0.1214159 2.332712 at 90iterations 7.0030235E-02 1.449189 at 100iterations 4.0084027E-02 0.7774849 at 110iterations 2.3045063E-02 0.4407377 at 120iterations 1.3219561E-02 0.3132229 at 130iterations 7.5807539E-03 0.1418457 at 140iterations 4.3375022E-03 8.4875107E-02 at 150iterations 2.4831900E-03 4.7821045E-02 at 160iterations 1.4262070E-03 2.5348306E-02 at 170iterations 8.1573997E-04 1.6757965E-02 at 180iterations finished qdiffx linear iterations at : 14:39:55 total time elapsed so far: 15.62000 # loops : 180 mean,max change (kT/e) : 8.1573997E-04 1.6757965E-02 energy calculations done at 15.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.80000 DelPhi exited at 14:39:56 15.805u 0.313s 0:16.46 97.8% 0+0k 0+0io 0pf+0w