Tue Oct 11 04:45:58 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 Tue Oct 11 2011 at 04:45:58 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6465204 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): -11.90300 36.32700 ymin,ymax (A): -25.88500 22.49300 zmin,zma (A): -9.678000 45.38600 x,y,z range (A): 48.23000 48.37800 55.06400 scale (grids/A): 0.6465204 object centre (A): 12.21200 -1.696000 17.85400 number of atom coordinates read : 2755 total number of charged atoms : 2603 net assigned charge : 3.176013 assigned positive charge : 418.8128 centred at (gu) : 90.31816 90.51425 91.86423 assigned negative charge : -415.6373 centred at (gu) : 90.06533 90.32603 91.80404 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7594 nv = 96 ne = 84 npr = 56645 no. pairs analyzed = 56645 no. exposed pairs = 3344 no. arc points = 23592 no. surface atoms = 1123 nbur = 1632 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 4256 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.3500000 number of dielectric boundary points 3695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2309 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5007953E-09 2.0903382E-08 midg,1,midg; midg,igrid,midg -2.0883643E-08 3.6324042E-08 1,midg,midg; igrid,midg,midg -3.1188307E-08 4.4619174E-08 gauss-seidel spectral radius is 0.9876120 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 04:45:59 rms-change max change #iterations 0.1592959 20.87137 at 10iterations 1.6396374E-02 2.341583 at 20iterations 1.7029999E-03 0.2174911 at 30iterations 1.7501182E-04 3.4198761E-02 at 40iterations 1.9093708E-05 2.2411346E-03 at 50iterations finished qdiffx linear iterations at : 04:46:01 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 1.9093708E-05 2.2411346E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 04:46:02 3.194u 0.150s 0:03.70 90.2% 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 Tue Oct 11 2011 at 04:46:02 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.939561 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): -11.90300 36.32700 ymin,ymax (A): -25.88500 22.49300 zmin,zma (A): -9.678000 45.38600 x,y,z range (A): 48.23000 48.37800 55.06400 scale (grids/A): 1.939561 object centre (A): 12.21200 -1.696000 17.85400 number of atom coordinates read : 2755 total number of charged atoms : 2603 net assigned charge : 3.176013 assigned positive charge : 418.8128 centred at (gu) : 90.95399 91.54241 95.59208 assigned negative charge : -415.6373 centred at (gu) : 90.19556 90.97781 95.41183 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23592 grid for indexing accessible points = 1.400000 m= 29922 mr = 57829 m= 4557 mr = 22100 m= 273 mr = 2806 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1733 time to turn everything in is 0.5500000 number of dielectric boundary points 33927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20491 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) : 0.6465204 object centre at (A) : 12.21200 -1.696000 17.85400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5611168E-02 7.6696924E-03 midg,1,midg; midg,igrid,midg -1.4551011E-02 2.5963439E-02 1,midg,midg; igrid,midg,midg -6.5194056E-03 5.6405976E-02 gauss-seidel spectral radius is 0.9986949 estimated iterations to convergence 219 setup time was (sec) 0.9000000 now iterating at: 04:46:03 rms-change max change #iterations 4.596238 203.6509 at 10iterations 2.196259 75.56353 at 20iterations 1.050910 36.49022 at 30iterations 0.5010874 15.00963 at 40iterations 0.2391699 7.414494 at 50iterations 0.1142469 3.896801 at 60iterations 5.4556943E-02 1.594507 at 70iterations 2.5971783E-02 0.8055801 at 80iterations 1.2408872E-02 0.3763123 at 90iterations 5.9189335E-03 0.1713257 at 100iterations 2.8305210E-03 8.4200859E-02 at 110iterations 1.3506713E-03 3.9260864E-02 at 120iterations finished qdiffx linear iterations at : 04:46:09 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.3506713E-03 3.9260864E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 04:46:10 7.466u 0.168s 0:08.04 94.7% 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 Tue Oct 11 2011 at 04:46:10 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.909342 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): -11.90300 36.32700 ymin,ymax (A): -25.88500 22.49300 zmin,zma (A): -9.678000 45.38600 x,y,z range (A): 48.23000 48.37800 55.06400 scale (grids/A): 2.909342 object centre (A): 12.21200 -1.696000 17.85400 number of atom coordinates read : 2755 total number of charged atoms : 2603 net assigned charge : 3.176013 assigned positive charge : 418.8128 centred at (gu) : 91.43089 92.31326 98.38802 assigned negative charge : -415.6373 centred at (gu) : 90.29333 91.46658 98.11768 start vw surface at 0.2200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 189672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23592 grid for indexing accessible points = 1.400000 m= 96901 mr = 139760 m= 34499 mr = 79727 m= 7967 mr = 27673 m= 1089 mr = 5868 m= 69 mr = 683 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 5790 time to turn everything in is 1.490000 number of dielectric boundary points 76462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 20812 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) : 1.939561 object centre at (A) : 12.21200 -1.696000 17.85400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5384314 0.3537655 midg,1,midg; midg,igrid,midg -0.1583476 0.3002319 1,midg,midg; igrid,midg,midg -3.5582669E-02 0.4340809 gauss-seidel spectral radius is 0.9992720 estimated iterations to convergence 292 setup time was (sec) 1.760000 now iterating at: 04:46:12 rms-change max change #iterations 10.68891 516.5076 at 10iterations 6.255687 142.9264 at 20iterations 3.653856 72.37273 at 30iterations 2.128710 44.20231 at 40iterations 1.241671 23.80830 at 50iterations 0.7207074 12.46088 at 60iterations 0.4182815 7.870891 at 70iterations 0.2424796 4.413259 at 80iterations 0.1406775 2.869101 at 90iterations 8.1410006E-02 1.466415 at 100iterations 4.7153126E-02 0.9534950 at 110iterations 2.7283050E-02 0.4624596 at 120iterations 1.5822709E-02 0.2631197 at 130iterations 9.1724480E-03 0.1553154 at 140iterations 5.3189364E-03 0.1130781 at 150iterations 3.0993605E-03 5.3718567E-02 at 160iterations 1.8091646E-03 3.5211563E-02 at 170iterations 1.0626593E-03 1.9493580E-02 at 180iterations finished qdiffx linear iterations at : 04:46:22 total time elapsed so far: 11.46000 # loops : 180 mean,max change (kT/e) : 1.0626593E-03 1.9493580E-02 energy calculations done at 11.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 04:46:22 11.637u 0.196s 0:12.36 95.6% 0+0k 0+0io 0pf+0w