Sun Oct 9 14:02:58 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 Sun Oct 9 2011 at 14:02:58 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.6810790 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): 21.50700 70.48200 ymin,ymax (A): -1.953000 50.31700 zmin,zma (A): -5.664000 37.46000 x,y,z range (A): 48.97500 52.27000 43.12400 scale (grids/A): 0.6810790 object centre (A): 45.99450 24.18200 15.89800 number of atom coordinates read : 2378 total number of charged atoms : 2232 net assigned charge : 3.406023 assigned positive charge : 365.6061 centred at (gu) : 90.36149 89.10413 89.01336 assigned negative charge : -362.2005 centred at (gu) : 90.38031 88.96503 88.92272 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7446 nv = 96 ne = 84 npr = 47806 no. pairs analyzed = 47806 no. exposed pairs = 2857 no. arc points = 20434 no. surface atoms = 966 nbur = 1412 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4193 m= 0 mr = 52 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.1800000 number of dielectric boundary points 3650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1982 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8545 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5698104E-08 3.5891741E-08 midg,1,midg; midg,igrid,midg -3.3977276E-08 4.8797457E-08 1,midg,midg; igrid,midg,midg 2.0192166E-08 1.0688668E-08 gauss-seidel spectral radius is 0.9888017 estimated iterations to convergence 77 setup time was (sec) 0.3700000 now iterating at: 14:02:59 rms-change max change #iterations 0.1859881 27.66295 at 10iterations 2.1004932E-02 3.651638 at 20iterations 2.5365211E-03 0.4234772 at 30iterations 3.6659895E-04 6.4006805E-02 at 40iterations 7.9047073E-05 1.2617111E-02 at 50iterations finished qdiffx linear iterations at : 14:03:02 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.9047073E-05 1.2617111E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:03:02 3.397u 0.178s 0:03.84 92.7% 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 Sun Oct 9 2011 at 14:03:02 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.043237 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): 21.50700 70.48200 ymin,ymax (A): -1.953000 50.31700 zmin,zma (A): -5.664000 37.46000 x,y,z range (A): 48.97500 52.27000 43.12400 scale (grids/A): 2.043237 object centre (A): 45.99450 24.18200 15.89800 number of atom coordinates read : 2378 total number of charged atoms : 2232 net assigned charge : 3.406023 assigned positive charge : 365.6061 centred at (gu) : 91.08364 87.31209 87.03968 assigned negative charge : -362.2005 centred at (gu) : 91.14059 86.89489 86.76775 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20434 grid for indexing accessible points = 1.400000 m= 29814 mr = 55819 m= 5056 mr = 22369 m= 419 mr = 3128 m= 8 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2223 time to turn everything in is 0.3900000 number of dielectric boundary points 33381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17665 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) : 0.6810790 object centre at (A) : 45.99450 24.18200 15.89800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2745980E-03 4.5902837E-02 midg,1,midg; midg,igrid,midg -4.3786038E-02 1.0518282E-02 1,midg,midg; igrid,midg,midg 3.4296043E-02 -1.3684100E-02 gauss-seidel spectral radius is 0.9987852 estimated iterations to convergence 227 setup time was (sec) 0.6200000 now iterating at: 14:03:03 rms-change max change #iterations 4.704470 221.7525 at 10iterations 2.292856 77.46191 at 20iterations 1.121182 36.00982 at 30iterations 0.5498126 15.74146 at 40iterations 0.2687805 7.582470 at 50iterations 0.1314315 3.752419 at 60iterations 6.4306132E-02 1.819402 at 70iterations 3.1456877E-02 1.029411 at 80iterations 1.5511163E-02 0.4714584 at 90iterations 7.5995792E-03 0.2080228 at 100iterations 3.7505643E-03 0.1127543 at 110iterations 1.8740685E-03 5.6252480E-02 at 120iterations finished qdiffx linear iterations at : 14:03:10 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.8740685E-03 5.6252480E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 14:03:11 7.885u 0.215s 0:08.35 96.8% 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 14:03:11 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.064856 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): 21.50700 70.48200 ymin,ymax (A): -1.953000 50.31700 zmin,zma (A): -5.664000 37.46000 x,y,z range (A): 48.97500 52.27000 43.12400 scale (grids/A): 3.064856 object centre (A): 45.99450 24.18200 15.89800 number of atom coordinates read : 2378 total number of charged atoms : 2232 net assigned charge : 3.406023 assigned positive charge : 365.6061 centred at (gu) : 91.62534 85.96809 85.55936 assigned negative charge : -362.2005 centred at (gu) : 91.71078 85.34227 85.15151 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 183708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20434 grid for indexing accessible points = 1.400000 m= 95882 mr = 134722 m= 35828 mr = 79329 m= 9164 mr = 29108 m= 1630 mr = 6842 m= 164 mr = 1120 m= 4 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 7671 time to turn everything in is 1.030000 number of dielectric boundary points 75169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17856 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) : 2.043237 object centre at (A) : 45.99450 24.18200 15.89800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2988398E-02 0.4315940 midg,1,midg; midg,igrid,midg -0.5575719 0.3025638 1,midg,midg; igrid,midg,midg 0.3591318 -0.3663472 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.270000 now iterating at: 14:03:12 rms-change max change #iterations 10.68039 409.2781 at 10iterations 6.285318 141.0455 at 20iterations 3.693509 73.25166 at 30iterations 2.164625 43.53302 at 40iterations 1.268167 23.45603 at 50iterations 0.7420678 13.82604 at 60iterations 0.4324890 7.542571 at 70iterations 0.2524515 4.693722 at 80iterations 0.1469510 2.830011 at 90iterations 8.5609600E-02 1.504397 at 100iterations 4.9839135E-02 0.8538437 at 110iterations 2.9001504E-02 0.4966621 at 120iterations 1.6896158E-02 0.2866335 at 130iterations 9.8713851E-03 0.1848660 at 140iterations 5.7666982E-03 0.1070480 at 150iterations 3.3908584E-03 5.5723190E-02 at 160iterations 2.0164102E-03 3.5003662E-02 at 170iterations 1.2183249E-03 2.1734238E-02 at 180iterations finished qdiffx linear iterations at : 14:03:23 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 1.2183249E-03 2.1734238E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 14:03:24 12.850u 0.218s 0:13.38 97.6% 0+0k 0+0io 0pf+0w