Sat Oct 15 12:59:28 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 15 2011 at 12:59:28 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 = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6177017 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): 21.65400 69.89300 ymin,ymax (A): -26.31900 27.68100 zmin,zma (A): -13.29500 44.33800 x,y,z range (A): 48.23900 54.00000 57.63300 scale (grids/A): 0.6177017 object centre (A): 45.77350 0.6809998 15.52150 number of atom coordinates read : 2711 total number of charged atoms : 2572 net assigned charge : 3.500008 assigned positive charge : 409.3504 centred at (gu) : 89.55184 90.13167 89.05918 assigned negative charge : -405.8514 centred at (gu) : 89.42284 90.12257 88.95616 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6793 nv = 96 ne = 84 npr = 54852 no. pairs analyzed = 54852 no. exposed pairs = 3509 no. arc points = 24189 no. surface atoms = 1175 nbur = 1536 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3561 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2100000 number of dielectric boundary points 3582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2413 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8429 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0178635E-09 7.6045579E-09 midg,1,midg; midg,igrid,midg 2.0948061E-09 3.4321892E-09 1,midg,midg; igrid,midg,midg -6.3858407E-09 9.9622151E-09 gauss-seidel spectral radius is 0.9864388 estimated iterations to convergence 70 setup time was (sec) 0.4400000 now iterating at: 12:59:29 rms-change max change #iterations 0.1238956 19.25510 at 10iterations 1.1360729E-02 1.683533 at 20iterations 1.0491444E-03 0.1550598 at 30iterations 9.7470111E-05 1.4623642E-02 at 40iterations 9.3835315E-06 1.2130737E-03 at 50iterations finished qdiffx linear iterations at : 12:59:32 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 9.3835315E-06 1.2130737E-03 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.960000 DelPhi exited at 12:59:32 3.963u 0.245s 0:04.51 93.1% 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 12:59:32 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 = 2711 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: 1.853105 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): 21.65400 69.89300 ymin,ymax (A): -26.31900 27.68100 zmin,zma (A): -13.29500 44.33800 x,y,z range (A): 48.23900 54.00000 57.63300 scale (grids/A): 1.853105 object centre (A): 45.77350 0.6809998 15.52150 number of atom coordinates read : 2711 total number of charged atoms : 2572 net assigned charge : 3.500008 assigned positive charge : 409.3504 centred at (gu) : 88.65456 90.39417 87.17706 assigned negative charge : -405.8514 centred at (gu) : 88.26834 90.36762 86.86823 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24189 grid for indexing accessible points = 1.400000 m= 25611 mr = 49520 m= 3882 mr = 18064 m= 229 mr = 2168 m= 3 mr = 65 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 0.3900000 number of dielectric boundary points 33080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20165 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) : 0.6177017 object centre at (A) : 45.77350 0.6809998 15.52150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9345233E-02 8.5197324E-03 midg,1,midg; midg,igrid,midg 1.7690111E-02 5.2099894E-03 1,midg,midg; igrid,midg,midg 3.5648094E-03 1.7202221E-02 gauss-seidel spectral radius is 0.9985780 estimated iterations to convergence 210 setup time was (sec) 0.6600000 now iterating at: 12:59:33 rms-change max change #iterations 4.103703 193.9036 at 10iterations 1.883697 71.12721 at 20iterations 0.8650126 29.00076 at 30iterations 0.3997962 12.14589 at 40iterations 0.1834161 6.372890 at 50iterations 8.4231600E-02 2.689101 at 60iterations 3.8872115E-02 1.251906 at 70iterations 1.7963566E-02 0.5779724 at 80iterations 8.2884477E-03 0.2814264 at 90iterations 3.8322369E-03 0.1168032 at 100iterations 1.7627008E-03 5.3562164E-02 at 110iterations 8.1267499E-04 2.7769566E-02 at 120iterations finished qdiffx linear iterations at : 12:59:42 total time elapsed so far: 9.100000 # loops : 120 mean,max change (kT/e) : 8.1267499E-04 2.7769566E-02 energy calculations done at 9.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.240000 DelPhi exited at 12:59:42 9.240u 0.292s 0:09.84 96.8% 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 12:59:42 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 = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.779658 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): 21.65400 69.89300 ymin,ymax (A): -26.31900 27.68100 zmin,zma (A): -13.29500 44.33800 x,y,z range (A): 48.23900 54.00000 57.63300 scale (grids/A): 2.779658 object centre (A): 45.77350 0.6809998 15.52150 number of atom coordinates read : 2711 total number of charged atoms : 2572 net assigned charge : 3.500008 assigned positive charge : 409.3504 centred at (gu) : 87.98177 90.59113 85.76531 assigned negative charge : -405.8514 centred at (gu) : 87.40237 90.55139 85.30227 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 168934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24189 grid for indexing accessible points = 1.400000 m= 83462 mr = 120319 m= 28910 mr = 66483 m= 6735 mr = 22318 m= 899 mr = 4653 m= 52 mr = 558 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 74650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 20569 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) : 1.853105 object centre at (A) : 45.77350 0.6809998 15.52150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7556247 0.1116463 midg,1,midg; midg,igrid,midg 0.1816494 4.4626594E-02 1,midg,midg; igrid,midg,midg 4.0748436E-02 0.1316840 gauss-seidel spectral radius is 0.9992470 estimated iterations to convergence 288 setup time was (sec) 1.300000 now iterating at: 12:59:44 rms-change max change #iterations 10.00527 315.5829 at 10iterations 5.927477 148.3007 at 20iterations 3.469072 79.63674 at 30iterations 2.026792 47.88362 at 40iterations 1.178084 24.14522 at 50iterations 0.6821590 13.57919 at 60iterations 0.3940734 8.190535 at 70iterations 0.2273165 4.549347 at 80iterations 0.1309835 2.562887 at 90iterations 7.5117774E-02 1.415804 at 100iterations 4.3058384E-02 0.8047600 at 110iterations 2.4837600E-02 0.4617462 at 120iterations 1.4237545E-02 0.2783089 at 130iterations 8.1551243E-03 0.1518962 at 140iterations 4.6717376E-03 9.4409943E-02 at 150iterations 2.6833182E-03 5.1150322E-02 at 160iterations 1.5361191E-03 2.8814316E-02 at 170iterations 8.8142481E-04 1.7112732E-02 at 180iterations finished qdiffx linear iterations at : 12:59:58 total time elapsed so far: 15.26000 # loops : 180 mean,max change (kT/e) : 8.8142481E-04 1.7112732E-02 energy calculations done at 15.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.39000 DelPhi exited at 12:59:58 15.395u 0.318s 0:16.13 97.3% 0+0k 0+0io 0pf+0w