Mon Oct 10 19:36:09 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 19:36:09 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2535 !!! WARNING: HIR 102 has a net charge of 0.5140 !!! WARNING: HIR 228 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: 0.6344454 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): -10.12200 45.78200 ymin,ymax (A): 32.37000 81.23200 zmin,zma (A): -10.55800 45.55400 x,y,z range (A): 55.90400 48.86200 56.11200 scale (grids/A): 0.6344454 object centre (A): 17.83000 56.80100 17.49800 number of atom coordinates read : 2535 total number of charged atoms : 2398 net assigned charge : -1.971988 assigned positive charge : 375.9310 centred at (gu) : 88.94177 89.33356 89.85771 assigned negative charge : -377.9039 centred at (gu) : 88.90978 89.43312 89.83649 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7060 nv = 96 ne = 84 npr = 50670 no. pairs analyzed = 50670 no. exposed pairs = 3587 no. arc points = 25369 no. surface atoms = 1197 nbur = 1338 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3475 m= 5 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2481 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8305 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6804942E-09 -3.9723311E-10 midg,1,midg; midg,igrid,midg 8.2749150E-09 -1.0620410E-08 1,midg,midg; igrid,midg,midg -7.0339965E-09 4.8103715E-10 gauss-seidel spectral radius is 0.9871404 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 19:36:10 rms-change max change #iterations 0.1379447 19.85101 at 10iterations 1.3235183E-02 1.925858 at 20iterations 1.2951838E-03 0.2407543 at 30iterations 1.3084104E-04 1.9361734E-02 at 40iterations 1.4773870E-05 2.7017593E-03 at 50iterations finished qdiffx linear iterations at : 19:36:12 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.4773870E-05 2.7017593E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 19:36:13 3.439u 0.190s 0:03.94 91.8% 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 Mon Oct 10 2011 at 19:36:13 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2535 !!! WARNING: HIR 102 has a net charge of 0.5140 !!! WARNING: HIR 228 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: 1.903336 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): -10.12200 45.78200 ymin,ymax (A): 32.37000 81.23200 zmin,zma (A): -10.55800 45.55400 x,y,z range (A): 55.90400 48.86200 56.11200 scale (grids/A): 1.903336 object centre (A): 17.83000 56.80100 17.49800 number of atom coordinates read : 2535 total number of charged atoms : 2398 net assigned charge : -1.971988 assigned positive charge : 375.9310 centred at (gu) : 86.82465 88.00018 89.57260 assigned negative charge : -377.9039 centred at (gu) : 86.72936 88.29930 89.50938 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25369 grid for indexing accessible points = 1.400000 m= 26446 mr = 49139 m= 4287 mr = 18209 m= 266 mr = 2516 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 36444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18897 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) : 0.6344454 object centre at (A) : 17.83000 56.80100 17.49800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8543683E-02 -3.1188071E-02 midg,1,midg; midg,igrid,midg 3.5961967E-02 -1.4519960E-02 1,midg,midg; igrid,midg,midg -1.9886880E-03 3.9312784E-03 gauss-seidel spectral radius is 0.9986499 estimated iterations to convergence 216 setup time was (sec) 0.8500000 now iterating at: 19:36:14 rms-change max change #iterations 4.177955 176.1048 at 10iterations 1.957225 68.27640 at 20iterations 0.9173788 30.96321 at 30iterations 0.4286043 13.56309 at 40iterations 0.2017529 6.869452 at 50iterations 9.4472431E-02 3.107111 at 60iterations 4.4370700E-02 1.417001 at 70iterations 2.0834159E-02 0.7122760 at 80iterations 9.7872913E-03 0.3173704 at 90iterations 4.6015703E-03 0.1544113 at 100iterations 2.1655681E-03 7.4728012E-02 at 110iterations 1.0156441E-03 3.4393311E-02 at 120iterations finished qdiffx linear iterations at : 19:36:22 total time elapsed so far: 8.470000 # loops : 120 mean,max change (kT/e) : 1.0156441E-03 3.4393311E-02 energy calculations done at 8.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 19:36:23 8.642u 0.260s 0:09.52 93.4% 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 19:36:23 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2535 !!! WARNING: HIR 102 has a net charge of 0.5140 !!! WARNING: HIR 228 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: 2.855004 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): -10.12200 45.78200 ymin,ymax (A): 32.37000 81.23200 zmin,zma (A): -10.55800 45.55400 x,y,z range (A): 55.90400 48.86200 56.11200 scale (grids/A): 2.855004 object centre (A): 17.83000 56.80100 17.49800 number of atom coordinates read : 2535 total number of charged atoms : 2398 net assigned charge : -1.971988 assigned positive charge : 375.9310 centred at (gu) : 85.23675 87.00011 89.35883 assigned negative charge : -377.9039 centred at (gu) : 85.09397 87.44890 89.26409 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 174289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25369 grid for indexing accessible points = 1.400000 m= 84353 mr = 120174 m= 30961 mr = 66108 m= 7694 mr = 23757 m= 1076 mr = 5459 m= 58 mr = 676 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 82234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19184 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) : 1.903336 object centre at (A) : 17.83000 56.80100 17.49800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1742420 -0.2751201 midg,1,midg; midg,igrid,midg 0.5011011 -0.1042636 1,midg,midg; igrid,midg,midg 0.3231689 2.9472124E-02 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 1.690000 now iterating at: 19:36:25 rms-change max change #iterations 10.02995 365.6190 at 10iterations 5.977286 178.2024 at 20iterations 3.515129 79.00398 at 30iterations 2.058698 44.25583 at 40iterations 1.203343 25.66311 at 50iterations 0.7017568 13.99594 at 60iterations 0.4069110 7.563875 at 70iterations 0.2363504 4.541225 at 80iterations 0.1370016 2.843178 at 90iterations 7.9320304E-02 1.487812 at 100iterations 4.5977935E-02 0.9474789 at 110iterations 2.6634995E-02 0.4987850 at 120iterations 1.5422282E-02 0.2807922 at 130iterations 8.9134779E-03 0.1686044 at 140iterations 5.1721525E-03 9.2972755E-02 at 150iterations 2.9958799E-03 5.5631638E-02 at 160iterations 1.7425010E-03 3.3336639E-02 at 170iterations 1.0153464E-03 1.8653870E-02 at 180iterations finished qdiffx linear iterations at : 19:36:36 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 1.0153464E-03 1.8653870E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 19:36:36 13.045u 0.259s 0:13.62 97.5% 0+0k 0+0io 0pf+0w