Mon Oct 10 14:02:31 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 Mon Oct 10 2011 at 14:02:32 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 = 2815 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: 0.5443592 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): -43.63900 21.75900 ymin,ymax (A): 110.8280 166.1070 zmin,zma (A): 155.8160 208.4860 x,y,z range (A): 65.39799 55.27900 52.67001 scale (grids/A): 0.5443592 object centre (A): -10.94000 138.4675 182.1510 number of atom coordinates read : 2815 total number of charged atoms : 2665 net assigned charge : 8.000022 assigned positive charge : 407.6080 centred at (gu) : 88.68552 89.55788 87.25706 assigned negative charge : -399.6084 centred at (gu) : 88.52895 89.50096 87.08616 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5633 nv = 96 ne = 84 npr = 53994 no. pairs analyzed = 53994 no. exposed pairs = 4211 no. arc points = 30677 no. surface atoms = 1393 nbur = 1422 mkacc time = 0.1600000 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 = 1.568000 m= 255 mr = 2487 m= 0 mr = 6 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2984 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7238 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6318487E-10 7.3351064E-10 midg,1,midg; midg,igrid,midg 2.0928166E-10 7.3613121E-10 1,midg,midg; igrid,midg,midg -5.3812466E-10 9.8232511E-10 gauss-seidel spectral radius is 0.9826078 estimated iterations to convergence 62 setup time was (sec) 0.6500000 now iterating at: 14:02:33 rms-change max change #iterations 6.8772897E-02 11.81253 at 10iterations 4.4950331E-03 0.7698431 at 20iterations 3.0725778E-04 5.0807953E-02 at 30iterations 3.1028954E-05 4.5223236E-03 at 40iterations 5.9774338E-06 7.9396367E-04 at 50iterations finished qdiffx linear iterations at : 14:02:37 total time elapsed so far: 4.800000 # loops : 50 mean,max change (kT/e) : 5.9774338E-06 7.9396367E-04 energy calculations done at 4.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 14:02:37 5.006u 0.391s 0:05.74 93.9% 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 14:02:37 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 = 2815 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: 1.633078 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): -43.63900 21.75900 ymin,ymax (A): 110.8280 166.1070 zmin,zma (A): 155.8160 208.4860 x,y,z range (A): 65.39799 55.27900 52.67001 scale (grids/A): 1.633078 object centre (A): -10.94000 138.4675 182.1510 number of atom coordinates read : 2815 total number of charged atoms : 2665 net assigned charge : 8.000022 assigned positive charge : 407.6080 centred at (gu) : 86.05588 88.67329 81.77061 assigned negative charge : -399.6084 centred at (gu) : 85.58646 88.50287 81.25801 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 60830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30677 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18526 mr = 37234 m= 1969 mr = 11755 m= 60 mr = 802 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 406 time to turn everything in is 0.6200000 number of dielectric boundary points 31590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20444 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) : 0.5443592 object centre at (A) : -10.94000 138.4675 182.1510 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4940347E-03 8.5854745E-03 midg,1,midg; midg,igrid,midg 1.1269585E-02 1.7441310E-02 1,midg,midg; igrid,midg,midg -2.1040805E-02 1.8249130E-02 gauss-seidel spectral radius is 0.9981872 estimated iterations to convergence 187 setup time was (sec) 1.010000 now iterating at: 14:02:39 rms-change max change #iterations 3.126766 168.1053 at 10iterations 1.295960 64.55579 at 20iterations 0.5372800 19.67186 at 30iterations 0.2230483 8.538194 at 40iterations 9.2635028E-02 3.426069 at 50iterations 3.8637705E-02 1.418159 at 60iterations 1.6043896E-02 0.6025014 at 70iterations 6.6760303E-03 0.2458951 at 80iterations 2.7718467E-03 0.1040542 at 90iterations 1.1621752E-03 4.2667389E-02 at 100iterations 4.8436638E-04 1.8656731E-02 at 110iterations 2.0305383E-04 7.7486038E-03 at 120iterations finished qdiffx linear iterations at : 14:02:49 total time elapsed so far: 11.55000 # loops : 120 mean,max change (kT/e) : 2.0305383E-04 7.7486038E-03 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 14:02:50 11.743u 0.480s 0:12.99 94.0% 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 14:02:51 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 = 2815 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: 2.449616 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): -43.63900 21.75900 ymin,ymax (A): 110.8280 166.1070 zmin,zma (A): 155.8160 208.4860 x,y,z range (A): 65.39799 55.27900 52.67001 scale (grids/A): 2.449616 object centre (A): -10.94000 138.4675 182.1510 number of atom coordinates read : 2815 total number of charged atoms : 2665 net assigned charge : 8.000022 assigned positive charge : 407.6080 centred at (gu) : 84.08363 88.00958 77.65592 assigned negative charge : -399.6084 centred at (gu) : 83.37961 87.75428 76.88695 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 140702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30677 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 62479 mr = 92086 m= 18414 mr = 46555 m= 2897 mr = 12993 m= 184 mr = 1617 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 1331 time to turn everything in is 1.470000 number of dielectric boundary points 71355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 21304 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) : 1.633078 object centre at (A) : -10.94000 138.4675 182.1510 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8984242E-02 0.1111607 midg,1,midg; midg,igrid,midg 0.1648380 0.3670848 1,midg,midg; igrid,midg,midg -0.6306601 0.7028055 gauss-seidel spectral radius is 0.9991434 estimated iterations to convergence 270 setup time was (sec) 1.890000 now iterating at: 14:02:53 rms-change max change #iterations 8.392516 308.9927 at 10iterations 4.813476 139.6557 at 20iterations 2.731424 90.98854 at 30iterations 1.536075 47.70163 at 40iterations 0.8582661 24.77364 at 50iterations 0.4790519 13.33719 at 60iterations 0.2664333 6.907371 at 70iterations 0.1481345 4.428925 at 80iterations 8.2004875E-02 2.054298 at 90iterations 4.5379292E-02 1.187003 at 100iterations 2.5063610E-02 0.6394222 at 110iterations 1.3817593E-02 0.3026638 at 120iterations 7.6216757E-03 0.1856918 at 130iterations 4.2195064E-03 9.9097729E-02 at 140iterations 2.3185569E-03 5.3863525E-02 at 150iterations 1.2799676E-03 2.8337479E-02 at 160iterations 7.0533645E-04 1.5316486E-02 at 170iterations 3.8856405E-04 9.1438293E-03 at 180iterations finished qdiffx linear iterations at : 14:03:12 total time elapsed so far: 20.53000 # loops : 180 mean,max change (kT/e) : 3.8856405E-04 9.1438293E-03 energy calculations done at 20.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.72000 DelPhi exited at 14:03:13 20.721u 0.589s 0:22.05 96.5% 0+0k 0+0io 0pf+0w