Sat Oct 8 18:25:43 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 8 2011 at 18:25:43 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5852279 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): -32.83000 25.29200 ymin,ymax (A): -2.698000 58.13300 zmin,zma (A): 3.939000 55.34900 x,y,z range (A): 58.12200 60.83100 51.41000 scale (grids/A): 0.5852279 object centre (A): -3.769001 27.71750 29.64400 number of atom coordinates read : 3315 total number of charged atoms : 3169 net assigned charge : -5.499984 assigned positive charge : 497.4587 centred at (gu) : 88.52579 90.59241 90.06854 assigned negative charge : -502.9599 centred at (gu) : 88.50692 90.55975 90.04124 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7616 nv = 96 ne = 84 npr = 67626 no. pairs analyzed = 67626 no. exposed pairs = 4069 no. arc points = 27978 no. surface atoms = 1387 nbur = 1928 mkacc time = 0.1500000 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= 337 mr = 4220 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9605 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2066320E-09 -6.3975886E-10 midg,1,midg; midg,igrid,midg -2.0965734E-09 -5.3364591E-10 1,midg,midg; igrid,midg,midg -2.7957776E-09 -6.3897582E-10 gauss-seidel spectral radius is 0.9849542 estimated iterations to convergence 67 setup time was (sec) 0.6100000 now iterating at: 18:25:44 rms-change max change #iterations 0.1102339 18.10442 at 10iterations 8.8633727E-03 1.331313 at 20iterations 7.9109235E-04 0.1105063 at 30iterations 1.1389575E-04 1.7078400E-02 at 40iterations 2.9277806E-05 4.9090385E-03 at 50iterations finished qdiffx linear iterations at : 18:25:47 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 2.9277806E-05 4.9090385E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 18:25:47 3.571u 0.230s 0:04.15 91.5% 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 8 2011 at 18:25:47 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.755684 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): -32.83000 25.29200 ymin,ymax (A): -2.698000 58.13300 zmin,zma (A): 3.939000 55.34900 x,y,z range (A): 58.12200 60.83100 51.41000 scale (grids/A): 1.755684 object centre (A): -3.769001 27.71750 29.64400 number of atom coordinates read : 3315 total number of charged atoms : 3169 net assigned charge : -5.499984 assigned positive charge : 497.4587 centred at (gu) : 85.57661 91.77635 90.20480 assigned negative charge : -502.9599 centred at (gu) : 85.52041 91.67878 90.12322 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27978 grid for indexing accessible points = 1.400000 m= 29511 mr = 58629 m= 3885 mr = 21448 m= 192 mr = 2204 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 0.6000000 number of dielectric boundary points 34299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 24649 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) : 0.5852279 object centre at (A) : -3.769001 27.71750 29.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2218227E-02 -8.9998785E-03 midg,1,midg; midg,igrid,midg -3.5555672E-02 -1.7826724E-03 1,midg,midg; igrid,midg,midg -1.3012245E-02 3.9017171E-04 gauss-seidel spectral radius is 0.9984686 estimated iterations to convergence 203 setup time was (sec) 0.9100000 now iterating at: 18:25:48 rms-change max change #iterations 4.144328 182.9168 at 10iterations 1.853890 58.94351 at 20iterations 0.8268147 25.84741 at 30iterations 0.3719322 11.58435 at 40iterations 0.1667124 5.196957 at 50iterations 7.4789196E-02 2.471451 at 60iterations 3.3457860E-02 1.178513 at 70iterations 1.5030654E-02 0.4490190 at 80iterations 6.7584650E-03 0.2053795 at 90iterations 3.0468381E-03 9.2536926E-02 at 100iterations 1.3740329E-03 4.1748047E-02 at 110iterations 6.2776706E-04 1.9926071E-02 at 120iterations finished qdiffx linear iterations at : 18:25:55 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 6.2776706E-04 1.9926071E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 18:25:56 8.163u 0.282s 0:08.72 96.7% 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 Sat Oct 8 2011 at 18:25:56 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.633526 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): -32.83000 25.29200 ymin,ymax (A): -2.698000 58.13300 zmin,zma (A): 3.939000 55.34900 x,y,z range (A): 58.12200 60.83100 51.41000 scale (grids/A): 2.633526 object centre (A): -3.769001 27.71750 29.64400 number of atom coordinates read : 3315 total number of charged atoms : 3169 net assigned charge : -5.499984 assigned positive charge : 497.4587 centred at (gu) : 83.36473 92.66440 90.30689 assigned negative charge : -502.9599 centred at (gu) : 83.28036 92.51821 90.18471 start vw surface at 0.1800000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 192256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27978 grid for indexing accessible points = 1.400000 m= 97790 mr = 142086 m= 32706 mr = 80088 m= 6606 mr = 25591 m= 781 mr = 4625 m= 19 mr = 443 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 1272 time to turn everything in is 1.500000 number of dielectric boundary points 77322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 25342 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) : 1.755684 object centre at (A) : -3.769001 27.71750 29.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3786925E-02 -0.1097160 midg,1,midg; midg,igrid,midg -0.4048622 -1.4896849E-02 1,midg,midg; igrid,midg,midg -0.1714514 -0.1865104 gauss-seidel spectral radius is 0.9992284 estimated iterations to convergence 284 setup time was (sec) 1.840000 now iterating at: 18:25:58 rms-change max change #iterations 10.13643 258.9122 at 10iterations 5.851686 141.5204 at 20iterations 3.345261 70.49930 at 30iterations 1.917294 35.28633 at 40iterations 1.091571 20.16953 at 50iterations 0.6223949 11.52194 at 60iterations 0.3548636 6.916183 at 70iterations 0.2023139 3.828974 at 80iterations 0.1149086 2.110374 at 90iterations 6.5366514E-02 1.206245 at 100iterations 3.7140392E-02 0.6632876 at 110iterations 2.1090291E-02 0.3950119 at 120iterations 1.1990502E-02 0.2018909 at 130iterations 6.8110353E-03 0.1215076 at 140iterations 3.8713089E-03 7.0672989E-02 at 150iterations 2.2066406E-03 3.7900925E-02 at 160iterations 1.2553777E-03 2.1484375E-02 at 170iterations 7.2111812E-04 1.3312340E-02 at 180iterations finished qdiffx linear iterations at : 18:26:09 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 7.2111812E-04 1.3312340E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 18:26:10 13.540u 0.280s 0:14.10 98.0% 0+0k 0+0io 0pf+0w