Mon Oct 10 13:59:17 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 Mon Oct 10 2011 at 13:59:17 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 !!! WARNING: SEP 288 has a net charge of -0.4750 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 0.5069275 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): -2.837000 67.39000 ymin,ymax (A): -12.53300 39.02300 zmin,zma (A): -24.66200 44.90200 x,y,z range (A): 70.22700 51.55600 69.56400 scale (grids/A): 0.5069275 object centre (A): 32.27650 13.24500 10.12000 number of atom coordinates read : 4389 total number of charged atoms : 4233 net assigned charge : -2.960947 assigned positive charge : 664.1591 centred at (gu) : 87.98412 90.00179 91.78573 assigned negative charge : -667.1224 centred at (gu) : 88.07163 90.12589 91.85864 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7037 nv = 96 ne = 84 npr = 92148 no. pairs analyzed = 92148 no. exposed pairs = 5026 no. arc points = 33601 no. surface atoms = 1718 nbur = 2671 mkacc time = 0.1600000 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 = 1.680000 m= 261 mr = 3958 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3000000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3407 ## 516 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9574 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9078979E-11 -3.0284089E-10 midg,1,midg; midg,igrid,midg 2.1388746E-10 -2.9473732E-10 1,midg,midg; igrid,midg,midg 2.4599853E-10 -1.2764480E-10 gauss-seidel spectral radius is 0.9800621 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 13:59:18 rms-change max change #iterations 6.3031599E-02 10.52195 at 10iterations 3.8300324E-03 0.5828209 at 20iterations 5.0523534E-04 6.2735081E-02 at 30iterations 1.3834836E-04 1.9783020E-02 at 40iterations 4.1605585E-05 6.3395500E-03 at 50iterations finished qdiffx linear iterations at : 13:59:21 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 4.1605585E-05 6.3395500E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 13:59:23 3.573u 0.180s 0:05.81 64.5% 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 Mon Oct 10 2011 at 13:59:23 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 !!! WARNING: SEP 288 has a net charge of -0.4750 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 1.520783 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): -2.837000 67.39000 ymin,ymax (A): -12.53300 39.02300 zmin,zma (A): -24.66200 44.90200 x,y,z range (A): 70.22700 51.55600 69.56400 scale (grids/A): 1.520783 object centre (A): 32.27650 13.24500 10.12000 number of atom coordinates read : 4389 total number of charged atoms : 4233 net assigned charge : -2.960947 assigned positive charge : 664.1591 centred at (gu) : 83.95161 90.00429 95.35619 assigned negative charge : -667.1224 centred at (gu) : 84.21444 90.37723 95.57548 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33601 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23962 mr = 58081 m= 2161 mr = 16866 m= 46 mr = 1095 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1365 time to turn everything in is 0.4000000 number of dielectric boundary points 30883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 463 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 31827 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) : 0.5069275 object centre at (A) : 32.27650 13.24500 10.12000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4888842E-03 -1.4246247E-02 midg,1,midg; midg,igrid,midg 3.6477025E-03 -9.8003652E-03 1,midg,midg; igrid,midg,midg 1.6539281E-02 -7.1222493E-03 gauss-seidel spectral radius is 0.9980199 estimated iterations to convergence 179 setup time was (sec) 0.6100000 now iterating at: 13:59:24 rms-change max change #iterations 3.554815 179.6421 at 10iterations 1.426192 51.59441 at 20iterations 0.5743698 19.34526 at 30iterations 0.2308141 8.756779 at 40iterations 9.2994280E-02 3.167765 at 50iterations 3.7353903E-02 1.201622 at 60iterations 1.5103622E-02 0.5187101 at 70iterations 6.1484878E-03 0.2222977 at 80iterations 2.5530809E-03 8.3037376E-02 at 90iterations 1.0972216E-03 3.8244247E-02 at 100iterations 5.1237078E-04 1.8278122E-02 at 110iterations 2.6400344E-04 8.8806152E-03 at 120iterations finished qdiffx linear iterations at : 13:59:31 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.6400344E-04 8.8806152E-03 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 13:59:31 7.765u 0.192s 0:08.42 94.4% 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 13:59:32 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 !!! WARNING: SEP 288 has a net charge of -0.4750 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 2.281174 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): -2.837000 67.39000 ymin,ymax (A): -12.53300 39.02300 zmin,zma (A): -24.66200 44.90200 x,y,z range (A): 70.22700 51.55600 69.56400 scale (grids/A): 2.281174 object centre (A): 32.27650 13.24500 10.12000 number of atom coordinates read : 4389 total number of charged atoms : 4233 net assigned charge : -2.960947 assigned positive charge : 664.1591 centred at (gu) : 80.92712 90.00629 98.03397 assigned negative charge : -667.1224 centred at (gu) : 81.32153 90.56582 98.36311 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 188680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33601 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86332 mr = 142177 m= 22074 mr = 69679 m= 3255 mr = 16685 m= 124 mr = 2191 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 4391 time to turn everything in is 0.9800000 number of dielectric boundary points 69720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 33768 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) : 1.520783 object centre at (A) : 32.27650 13.24500 10.12000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2373903 -0.3115002 midg,1,midg; midg,igrid,midg 3.8786240E-02 -0.1595159 1,midg,midg; igrid,midg,midg 0.3410661 -0.3106653 gauss-seidel spectral radius is 0.9991115 estimated iterations to convergence 265 setup time was (sec) 1.260000 now iterating at: 13:59:33 rms-change max change #iterations 9.565970 412.5947 at 10iterations 5.340731 130.1805 at 20iterations 2.963744 65.20815 at 30iterations 1.639504 34.35108 at 40iterations 0.9019528 18.92419 at 50iterations 0.4960811 9.591476 at 60iterations 0.2721664 5.377308 at 70iterations 0.1488079 2.852135 at 80iterations 8.1496939E-02 1.604157 at 90iterations 4.4650361E-02 0.8896819 at 100iterations 2.4407458E-02 0.4685059 at 110iterations 1.3394460E-02 0.2780228 at 120iterations 7.3616006E-03 0.1469231 at 130iterations 4.0668990E-03 7.9450607E-02 at 140iterations 2.2843666E-03 4.4406891E-02 at 150iterations 1.3069037E-03 2.5997162E-02 at 160iterations 7.7558291E-04 1.5289307E-02 at 170iterations 4.7867565E-04 9.0408325E-03 at 180iterations finished qdiffx linear iterations at : 13:59:45 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 4.7867565E-04 9.0408325E-03 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 13:59:46 12.892u 0.297s 0:14.29 92.2% 0+0k 0+0io 0pf+0w