Sat Oct 8 20:45:33 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 20:45:33 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 351 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6263415 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): -11.19300 38.86000 ymin,ymax (A): -22.02100 24.62000 zmin,zma (A): -12.11200 44.72600 x,y,z range (A): 50.05300 46.64100 56.83800 scale (grids/A): 0.6263415 object centre (A): 13.83350 1.299500 16.30700 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.73730 89.28471 89.72681 assigned negative charge : -387.9385 centred at (gu) : 88.63651 89.33309 89.60257 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6646 nv = 96 ne = 84 npr = 54406 no. pairs analyzed = 54406 no. exposed pairs = 3056 no. arc points = 21611 no. surface atoms = 1026 nbur = 1567 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3716 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.2800000 number of dielectric boundary points 3214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2145 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4891821E-09 1.2880378E-08 midg,1,midg; midg,igrid,midg 9.0607628E-09 7.7077025E-11 1,midg,midg; igrid,midg,midg -5.6277076E-09 9.0137995E-09 gauss-seidel spectral radius is 0.9867917 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 20:45:34 rms-change max change #iterations 0.1326944 19.58960 at 10iterations 1.2607102E-02 1.722584 at 20iterations 1.3644211E-03 0.2291813 at 30iterations 2.7181840E-04 5.6980133E-02 at 40iterations 8.5975553E-05 1.9336700E-02 at 50iterations finished qdiffx linear iterations at : 20:45:36 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 8.5975553E-05 1.9336700E-02 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 20:45:37 3.140u 0.169s 0:03.58 92.1% 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 8 2011 at 20:45:37 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 351 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.879025 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): -11.19300 38.86000 ymin,ymax (A): -22.02100 24.62000 zmin,zma (A): -12.11200 44.72600 x,y,z range (A): 50.05300 46.64100 56.83800 scale (grids/A): 1.879025 object centre (A): 13.83350 1.299500 16.30700 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 86.21179 87.85351 89.17997 assigned negative charge : -387.9385 centred at (gu) : 85.90923 87.99920 88.80773 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21611 grid for indexing accessible points = 1.400000 m= 25317 mr = 50443 m= 3797 mr = 18607 m= 180 mr = 2401 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2188 time to turn everything in is 0.5000000 number of dielectric boundary points 29798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19259 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) : 0.6263415 object centre at (A) : 13.83350 1.299500 16.30700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4625383E-02 2.0632617E-02 midg,1,midg; midg,igrid,midg 1.2491803E-02 1.0764301E-03 1,midg,midg; igrid,midg,midg -4.9061510E-03 3.6673900E-02 gauss-seidel spectral radius is 0.9985935 estimated iterations to convergence 211 setup time was (sec) 0.7700000 now iterating at: 20:45:38 rms-change max change #iterations 4.116686 196.1853 at 10iterations 1.907366 70.18463 at 20iterations 0.8806204 31.17991 at 30iterations 0.4082562 14.04995 at 40iterations 0.1893481 6.577947 at 50iterations 8.7558702E-02 2.940750 at 60iterations 4.0661208E-02 1.515251 at 70iterations 1.8915443E-02 0.5692673 at 80iterations 8.7868487E-03 0.2672148 at 90iterations 4.1048615E-03 0.1286602 at 100iterations 1.9464442E-03 6.2969208E-02 at 110iterations 9.5014612E-04 3.5279274E-02 at 120iterations finished qdiffx linear iterations at : 20:45:44 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 9.5014612E-04 3.5279274E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 20:45:45 7.130u 0.196s 0:07.68 95.3% 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 20:45:45 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 351 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.818537 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): -11.19300 38.86000 ymin,ymax (A): -22.02100 24.62000 zmin,zma (A): -12.11200 44.72600 x,y,z range (A): 50.05300 46.64100 56.83800 scale (grids/A): 2.818537 object centre (A): 13.83350 1.299500 16.30700 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 84.31746 86.78029 88.76994 assigned negative charge : -387.9385 centred at (gu) : 83.86373 86.99858 88.21151 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21611 grid for indexing accessible points = 1.400000 m= 83416 mr = 122112 m= 28952 mr = 68748 m= 6846 mr = 23162 m= 857 mr = 5136 m= 38 mr = 539 m= 1 mr = 9 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 7179 time to turn everything in is 1.230000 number of dielectric boundary points 67117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19600 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) : 1.879025 object centre at (A) : 13.83350 1.299500 16.30700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5818375E-02 0.2348464 midg,1,midg; midg,igrid,midg 0.1549586 -1.2002653E-02 1,midg,midg; igrid,midg,midg -6.3414447E-02 0.4762729 gauss-seidel spectral radius is 0.9992417 estimated iterations to convergence 287 setup time was (sec) 1.510000 now iterating at: 20:45:46 rms-change max change #iterations 9.655205 321.1725 at 10iterations 5.576568 125.6737 at 20iterations 3.202715 71.41049 at 30iterations 1.838386 36.25500 at 40iterations 1.054019 20.51754 at 50iterations 0.6023853 11.33897 at 60iterations 0.3457418 6.356102 at 70iterations 0.1974903 4.129837 at 80iterations 0.1129245 2.102245 at 90iterations 6.4548373E-02 1.377917 at 100iterations 3.6809597E-02 0.6956139 at 110iterations 2.1020116E-02 0.4113531 at 120iterations 1.2061809E-02 0.2459030 at 130iterations 6.9062118E-03 0.1375227 at 140iterations 3.9741350E-03 8.4311008E-02 at 150iterations 2.3054846E-03 4.9174309E-02 at 160iterations 1.3528952E-03 2.9613495E-02 at 170iterations 8.1978721E-04 1.8964767E-02 at 180iterations finished qdiffx linear iterations at : 20:45:56 total time elapsed so far: 11.22000 # loops : 180 mean,max change (kT/e) : 8.1978721E-04 1.8964767E-02 energy calculations done at 11.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 20:45:57 11.397u 0.211s 0:11.93 97.2% 0+0k 0+0io 0pf+0w