Sun Oct 9 15:28:59 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 Sun Oct 9 2011 at 15:28:59 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5530 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 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: 0.5153893 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): 26.46200 86.09200 ymin,ymax (A): 10.89100 79.96500 zmin,zma (A): -30.86600 33.57700 x,y,z range (A): 59.63000 69.07401 64.44300 scale (grids/A): 0.5153893 object centre (A): 56.27700 45.42800 1.355500 number of atom coordinates read : 5530 total number of charged atoms : 5359 net assigned charge : -4.399958 assigned positive charge : 847.0988 centred at (gu) : 90.74696 90.19881 89.32102 assigned negative charge : -851.5060 centred at (gu) : 90.67252 90.12881 89.40254 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8846 nv = 96 ne = 84 npr = 116020 no. pairs analyzed = 116020 no. exposed pairs = 6393 no. arc points = 43155 no. surface atoms = 2170 nbur = 3360 mkacc time = 0.2500000 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 = 1.652000 m= 341 mr = 4819 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4173 ## 555 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12000 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6829713E-10 -3.3008501E-10 midg,1,midg; midg,igrid,midg -3.3204425E-10 1.9046825E-10 1,midg,midg; igrid,midg,midg -3.0183805E-10 2.4128327E-10 gauss-seidel spectral radius is 0.9807817 estimated iterations to convergence 60 setup time was (sec) 0.7500000 now iterating at: 15:29:00 rms-change max change #iterations 8.0047235E-02 10.80637 at 10iterations 5.6535620E-03 0.9106445 at 20iterations 9.0910884E-04 0.1148987 at 30iterations 2.4273717E-04 3.1835556E-02 at 40iterations 7.1834031E-05 9.2067719E-03 at 50iterations finished qdiffx linear iterations at : 15:29:03 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 7.1834031E-05 9.2067719E-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) 3.560000 DelPhi exited at 15:29:03 3.568u 0.192s 0:04.03 93.0% 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 Sun Oct 9 2011 at 15:29:03 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5530 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 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: 1.546168 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): 26.46200 86.09200 ymin,ymax (A): 10.89100 79.96500 zmin,zma (A): -30.86600 33.57700 x,y,z range (A): 59.63000 69.07401 64.44300 scale (grids/A): 1.546168 object centre (A): 56.27700 45.42800 1.355500 number of atom coordinates read : 5530 total number of charged atoms : 5359 net assigned charge : -4.399958 assigned positive charge : 847.0988 centred at (gu) : 92.23911 90.59441 87.96102 assigned negative charge : -851.5060 centred at (gu) : 92.01741 90.38639 88.20721 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 99490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43155 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 30613 mr = 70021 m= 2953 mr = 21282 m= 61 mr = 1381 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 569 time to turn everything in is 0.7100000 number of dielectric boundary points 40433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 475 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 40290 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) : 0.5153893 object centre at (A) : 56.27700 45.42800 1.355500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8858762E-03 6.3293707E-03 midg,1,midg; midg,igrid,midg -1.5006350E-02 -2.5389548E-02 1,midg,midg; igrid,midg,midg -1.2137175E-02 1.0443897E-02 gauss-seidel spectral radius is 0.9981978 estimated iterations to convergence 187 setup time was (sec) 1.000000 now iterating at: 15:29:05 rms-change max change #iterations 4.306567 164.0188 at 10iterations 1.805758 53.84698 at 20iterations 0.7547644 22.08370 at 30iterations 0.3154962 9.366286 at 40iterations 0.1327225 3.918060 at 50iterations 5.5690583E-02 1.538410 at 60iterations 2.3493936E-02 0.6987639 at 70iterations 9.9810399E-03 0.3095627 at 80iterations 4.2469888E-03 0.1255112 at 90iterations 1.8473617E-03 5.8403015E-02 at 100iterations 8.2457776E-04 2.5554657E-02 at 110iterations 3.9343652E-04 1.2304008E-02 at 120iterations finished qdiffx linear iterations at : 15:29:12 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 3.9343652E-04 1.2304008E-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 15:29:12 8.161u 0.261s 0:08.77 96.0% 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 Sun Oct 9 2011 at 15:29:12 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5530 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 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: 2.319252 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): 26.46200 86.09200 ymin,ymax (A): 10.89100 79.96500 zmin,zma (A): -30.86600 33.57700 x,y,z range (A): 59.63000 69.07401 64.44300 scale (grids/A): 2.319252 object centre (A): 56.27700 45.42800 1.355500 number of atom coordinates read : 5530 total number of charged atoms : 5359 net assigned charge : -4.399958 assigned positive charge : 847.0988 centred at (gu) : 93.35809 90.89111 86.94122 assigned negative charge : -851.5060 centred at (gu) : 93.02591 90.57973 87.31072 start vw surface at 0.2000000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 231467 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43155 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 107424 mr = 171034 m= 29745 mr = 85609 m= 4634 mr = 22350 m= 255 mr = 2986 m= 6 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 1942 time to turn everything in is 1.670000 number of dielectric boundary points 91463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 42781 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) : 1.546168 object centre at (A) : 56.27700 45.42800 1.355500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5458671E-02 0.2890582 midg,1,midg; midg,igrid,midg -0.2133370 -0.7287896 1,midg,midg; igrid,midg,midg -0.1629148 0.2722438 gauss-seidel spectral radius is 0.9991983 estimated iterations to convergence 279 setup time was (sec) 2.000000 now iterating at: 15:29:14 rms-change max change #iterations 11.48933 291.7853 at 10iterations 6.664094 143.8372 at 20iterations 3.828754 82.04144 at 30iterations 2.189459 42.83632 at 40iterations 1.247497 23.96804 at 50iterations 0.7081680 12.65453 at 60iterations 0.4017857 7.164474 at 70iterations 0.2273475 3.913846 at 80iterations 0.1283680 2.403195 at 90iterations 7.2670683E-02 1.278862 at 100iterations 4.0976204E-02 0.6875076 at 110iterations 2.3136249E-02 0.4237094 at 120iterations 1.3046344E-02 0.2158194 at 130iterations 7.3666736E-03 0.1361389 at 140iterations 4.1581914E-03 6.7546844E-02 at 150iterations 2.3555346E-03 4.2816162E-02 at 160iterations 1.3398184E-03 2.1800995E-02 at 170iterations 7.6961244E-04 1.2954712E-02 at 180iterations finished qdiffx linear iterations at : 15:29:26 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 7.6961244E-04 1.2954712E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 15:29:26 13.498u 0.248s 0:14.03 97.8% 0+0k 0+0io 0pf+0w