Mon Oct 10 14:14:40 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 14:14:40 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5925137 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): -8.295000 51.78800 ymin,ymax (A): -16.39800 34.48500 zmin,zma (A): 77.69400 131.8210 x,y,z range (A): 60.08300 50.88300 54.12700 scale (grids/A): 0.5925137 object centre (A): 21.74650 9.043498 104.7575 number of atom coordinates read : 2790 total number of charged atoms : 2647 net assigned charge : -4.599987 assigned positive charge : 431.9684 centred at (gu) : 91.97662 89.35165 89.31918 assigned negative charge : -436.5692 centred at (gu) : 91.94032 89.46114 89.35670 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6462 nv = 96 ne = 84 npr = 54890 no. pairs analyzed = 54890 no. exposed pairs = 3834 no. arc points = 26487 no. surface atoms = 1288 nbur = 1502 mkacc time = 0.1000000 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 = 1.456000 m= 338 mr = 3193 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2100000 number of dielectric boundary points 3578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2715 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3594184E-10 -2.4060278E-09 midg,1,midg; midg,igrid,midg 2.2263795E-09 -4.4563095E-09 1,midg,midg; igrid,midg,midg -1.7748735E-09 -6.1818001E-10 gauss-seidel spectral radius is 0.9852830 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 14:14:41 rms-change max change #iterations 0.1098799 16.16139 at 10iterations 8.8536246E-03 1.628445 at 20iterations 7.8206981E-04 0.1267548 at 30iterations 1.0407187E-04 1.5476227E-02 at 40iterations 2.4156139E-05 3.2873154E-03 at 50iterations finished qdiffx linear iterations at : 14:14:44 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 2.4156139E-05 3.2873154E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 14:14:44 3.611u 0.214s 0:04.33 88.2% 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 Mon Oct 10 2011 at 14:14:44 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.777541 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): -8.295000 51.78800 ymin,ymax (A): -16.39800 34.48500 zmin,zma (A): 77.69400 131.8210 x,y,z range (A): 60.08300 50.88300 54.12700 scale (grids/A): 1.777541 object centre (A): 21.74650 9.043498 104.7575 number of atom coordinates read : 2790 total number of charged atoms : 2647 net assigned charge : -4.599987 assigned positive charge : 431.9684 centred at (gu) : 95.92927 88.05423 87.95686 assigned negative charge : -436.5692 centred at (gu) : 95.82060 88.38297 88.06973 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69214 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26487 grid for indexing accessible points = 1.400000 m= 24266 mr = 45484 m= 3544 mr = 16672 m= 144 mr = 1962 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 136 time to turn everything in is 0.3500000 number of dielectric boundary points 33021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20604 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) : 0.5925137 object centre at (A) : 21.74650 9.043498 104.7575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7339457E-02 -3.0991871E-02 midg,1,midg; midg,igrid,midg -1.4513619E-03 -1.9446574E-02 1,midg,midg; igrid,midg,midg 2.0256322E-02 2.7114470E-02 gauss-seidel spectral radius is 0.9984656 estimated iterations to convergence 202 setup time was (sec) 0.5700000 now iterating at: 14:14:45 rms-change max change #iterations 3.962487 191.6458 at 10iterations 1.763903 77.68230 at 20iterations 0.7849116 28.74453 at 30iterations 0.3507737 11.43028 at 40iterations 0.1563503 5.311347 at 50iterations 6.9859698E-02 2.464972 at 60iterations 3.1184103E-02 0.9776440 at 70iterations 1.3935861E-02 0.4731064 at 80iterations 6.2613972E-03 0.1996465 at 90iterations 2.7825718E-03 9.6006393E-02 at 100iterations 1.2562199E-03 4.1610718E-02 at 110iterations 5.6613784E-04 1.7987251E-02 at 120iterations finished qdiffx linear iterations at : 14:14:52 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 5.6613784E-04 1.7987251E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 14:14:54 7.913u 0.230s 0:09.13 89.1% 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 Mon Oct 10 2011 at 14:14:54 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.666312 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): -8.295000 51.78800 ymin,ymax (A): -16.39800 34.48500 zmin,zma (A): 77.69400 131.8210 x,y,z range (A): 60.08300 50.88300 54.12700 scale (grids/A): 2.666312 object centre (A): 21.74650 9.043498 104.7575 number of atom coordinates read : 2790 total number of charged atoms : 2647 net assigned charge : -4.599987 assigned positive charge : 431.9684 centred at (gu) : 98.89375 87.08125 86.93504 assigned negative charge : -436.5692 centred at (gu) : 98.73078 87.57440 87.10448 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 159863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26487 grid for indexing accessible points = 1.400000 m= 78188 mr = 111073 m= 27566 mr = 61187 m= 6218 mr = 21073 m= 679 mr = 4371 m= 17 mr = 353 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 0.9100000 number of dielectric boundary points 74474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 21167 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) : 1.777541 object centre at (A) : 21.74650 9.043498 104.7575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1889611 -0.3819155 midg,1,midg; midg,igrid,midg -3.8382087E-02 -0.1978665 1,midg,midg; igrid,midg,midg 0.4928212 0.2963080 gauss-seidel spectral radius is 0.9992194 estimated iterations to convergence 283 setup time was (sec) 1.150000 now iterating at: 14:14:55 rms-change max change #iterations 9.802503 265.9076 at 10iterations 5.693177 120.9523 at 20iterations 3.282797 76.34789 at 30iterations 1.884561 43.77549 at 40iterations 1.076937 22.22766 at 50iterations 0.6140715 12.07130 at 60iterations 0.3495918 7.202183 at 70iterations 0.1983922 3.960279 at 80iterations 0.1127531 2.403048 at 90iterations 6.3900456E-02 1.258556 at 100iterations 3.6231555E-02 0.6643126 at 110iterations 2.0548901E-02 0.3995018 at 120iterations 1.1629487E-02 0.2616282 at 130iterations 6.5911394E-03 0.1262951 at 140iterations 3.7410930E-03 7.9912186E-02 at 150iterations 2.1238257E-03 4.3384552E-02 at 160iterations 1.2081686E-03 2.4346352E-02 at 170iterations 6.9369288E-04 1.4495969E-02 at 180iterations finished qdiffx linear iterations at : 14:15:07 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 6.9369288E-04 1.4495969E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 14:15:08 13.021u 0.238s 0:13.99 94.7% 0+0k 0+0io 0pf+0w