Mon Oct 10 17:07:11 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 17:07:11 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4307 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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: 0.5137085 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): -15.93700 36.79000 ymin,ymax (A): -32.06700 31.40700 zmin,zma (A): -3.760000 65.54000 x,y,z range (A): 52.72700 63.47400 69.30000 scale (grids/A): 0.5137085 object centre (A): 10.42650 -0.3299990 30.89000 number of atom coordinates read : 4307 total number of charged atoms : 4105 net assigned charge : 0.9000361 assigned positive charge : 645.2203 centred at (gu) : 90.27016 90.64641 87.63543 assigned negative charge : -644.3243 centred at (gu) : 90.15612 90.70518 87.75831 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7128 nv = 96 ne = 84 npr = 87685 no. pairs analyzed = 87685 no. exposed pairs = 5597 no. arc points = 39005 no. surface atoms = 1866 nbur = 2441 mkacc time = 0.1500000 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= 261 mr = 3598 m= 0 mr = 5 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3797 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9662 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1846145E-10 -1.7432018E-10 midg,1,midg; midg,igrid,midg 1.3587828E-10 -1.7910104E-10 1,midg,midg; igrid,midg,midg -2.7967129E-10 3.2705846E-10 gauss-seidel spectral radius is 0.9805864 estimated iterations to convergence 59 setup time was (sec) 0.4700000 now iterating at: 17:07:11 rms-change max change #iterations 6.6233233E-02 9.808472 at 10iterations 3.8477106E-03 0.6035995 at 20iterations 2.7750112E-04 4.2331696E-02 at 30iterations 5.5078432E-05 7.0397258E-03 at 40iterations 1.7762384E-05 2.2374988E-03 at 50iterations finished qdiffx linear iterations at : 17:07:14 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.7762384E-05 2.2374988E-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) 3.510000 DelPhi exited at 17:07:15 3.513u 0.197s 0:04.06 91.1% 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 17:07:15 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4307 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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: 1.541125 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): -15.93700 36.79000 ymin,ymax (A): -32.06700 31.40700 zmin,zma (A): -3.760000 65.54000 x,y,z range (A): 52.72700 63.47400 69.30000 scale (grids/A): 1.541125 object centre (A): 10.42650 -0.3299990 30.89000 number of atom coordinates read : 4307 total number of charged atoms : 4105 net assigned charge : 0.9000361 assigned positive charge : 645.2203 centred at (gu) : 90.80886 91.93813 82.90508 assigned negative charge : -644.3243 centred at (gu) : 90.46799 92.11539 83.27456 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39005 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22939 mr = 54535 m= 2052 mr = 15080 m= 54 mr = 812 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.4000000 number of dielectric boundary points 35302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 537 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 30938 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) : 0.5137085 object centre at (A) : 10.42650 -0.3299990 30.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1954722E-03 -1.4723614E-02 midg,1,midg; midg,igrid,midg 4.2499087E-04 -5.8138794E-03 1,midg,midg; igrid,midg,midg -2.4343913E-03 9.0724677E-03 gauss-seidel spectral radius is 0.9980927 estimated iterations to convergence 182 setup time was (sec) 0.6200000 now iterating at: 17:07:16 rms-change max change #iterations 3.621849 144.2565 at 10iterations 1.472113 51.80688 at 20iterations 0.6006104 21.54476 at 30iterations 0.2447858 8.266785 at 40iterations 9.9786147E-02 3.648971 at 50iterations 4.0726729E-02 1.441984 at 60iterations 1.6690483E-02 0.5638809 at 70iterations 6.8514775E-03 0.2318273 at 80iterations 2.8134913E-03 0.1024551 at 90iterations 1.1705295E-03 3.6560059E-02 at 100iterations 4.9821316E-04 1.6441345E-02 at 110iterations 2.2489023E-04 7.3852539E-03 at 120iterations finished qdiffx linear iterations at : 17:07:23 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.2489023E-04 7.3852539E-03 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 17:07:23 7.927u 0.202s 0:08.51 95.4% 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 17:07:23 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4307 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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: 2.311688 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): -15.93700 36.79000 ymin,ymax (A): -32.06700 31.40700 zmin,zma (A): -3.760000 65.54000 x,y,z range (A): 52.72700 63.47400 69.30000 scale (grids/A): 2.311688 object centre (A): 10.42650 -0.3299990 30.89000 number of atom coordinates read : 4307 total number of charged atoms : 4105 net assigned charge : 0.9000361 assigned positive charge : 645.2203 centred at (gu) : 91.21308 92.90673 79.35728 assigned negative charge : -644.3243 centred at (gu) : 90.70214 93.17305 79.91179 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 187997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39005 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 82554 mr = 134410 m= 20727 mr = 63703 m= 2975 mr = 14703 m= 181 mr = 1806 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 547 time to turn everything in is 0.9600000 number of dielectric boundary points 79745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 32761 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) : 1.541125 object centre at (A) : 10.42650 -0.3299990 30.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1546875 -0.2988927 midg,1,midg; midg,igrid,midg -5.8150839E-02 -0.1565828 1,midg,midg; igrid,midg,midg -3.5075046E-02 0.1315601 gauss-seidel spectral radius is 0.9991484 estimated iterations to convergence 271 setup time was (sec) 1.200000 now iterating at: 17:07:25 rms-change max change #iterations 9.779611 310.4805 at 10iterations 5.578862 140.2842 at 20iterations 3.156133 74.93848 at 30iterations 1.776999 41.06590 at 40iterations 0.9985541 21.92999 at 50iterations 0.5569280 11.73351 at 60iterations 0.3111431 6.687851 at 70iterations 0.1731472 3.725338 at 80iterations 9.6193179E-02 2.144768 at 90iterations 5.3535305E-02 1.084322 at 100iterations 2.9618897E-02 0.6113739 at 110iterations 1.6453849E-02 0.3355141 at 120iterations 9.0758996E-03 0.2051659 at 130iterations 5.0345645E-03 0.1027985 at 140iterations 2.7862594E-03 6.1618805E-02 at 150iterations 1.5439133E-03 3.1866074E-02 at 160iterations 8.5146079E-04 1.8608093E-02 at 170iterations 4.7137879E-04 9.2926025E-03 at 180iterations finished qdiffx linear iterations at : 17:07:37 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 4.7137879E-04 9.2926025E-03 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 17:07:37 12.957u 0.226s 0:13.47 97.7% 0+0k 0+0io 0pf+0w