Mon Oct 10 14:05:11 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+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 14:05:11 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: SEP 107 has a net charge of -0.4750 !!! WARNING: SEP 739 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5195185 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): 28.22800 96.75300 ymin,ymax (A): 17.48400 80.75400 zmin,zma (A): 0.9569999 54.90500 x,y,z range (A): 68.52499 63.27000 53.94800 scale (grids/A): 0.5195185 object centre (A): 62.49050 49.11900 27.93100 number of atom coordinates read : 4549 total number of charged atoms : 4384 net assigned charge : 5.050025 assigned positive charge : 690.8055 centred at (gu) : 89.27984 91.34249 89.95009 assigned negative charge : -685.7604 centred at (gu) : 89.19395 91.49649 90.03318 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8030 nv = 96 ne = 84 npr = 87872 no. pairs analyzed = 87872 no. exposed pairs = 6182 no. arc points = 44051 no. surface atoms = 2061 nbur = 2488 mkacc time = 0.2100000 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= 267 mr = 3849 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4395 ## 690 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1944420E-10 -1.8379062E-10 midg,1,midg; midg,igrid,midg 4.6758952E-10 -6.4630457E-10 1,midg,midg; igrid,midg,midg -2.3904129E-10 3.5170142E-10 gauss-seidel spectral radius is 0.9810482 estimated iterations to convergence 60 setup time was (sec) 0.7100000 now iterating at: 14:05:12 rms-change max change #iterations 7.1058989E-02 15.19984 at 10iterations 4.1838749E-03 0.7601166 at 20iterations 3.2079237E-04 4.6720505E-02 at 30iterations 7.3340925E-05 1.5162468E-02 at 40iterations 2.5682586E-05 5.4650307E-03 at 50iterations finished qdiffx linear iterations at : 14:05:15 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 2.5682586E-05 5.4650307E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:05:15 3.760u 0.225s 0:04.32 92.1% 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 14:05:15 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: SEP 107 has a net charge of -0.4750 !!! WARNING: SEP 739 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.558555 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): 28.22800 96.75300 ymin,ymax (A): 17.48400 80.75400 zmin,zma (A): 0.9569999 54.90500 x,y,z range (A): 68.52499 63.27000 53.94800 scale (grids/A): 1.558555 object centre (A): 62.49050 49.11900 27.93100 number of atom coordinates read : 4549 total number of charged atoms : 4384 net assigned charge : 5.050025 assigned positive charge : 690.8055 centred at (gu) : 87.83772 94.02541 89.84833 assigned negative charge : -685.7604 centred at (gu) : 87.58147 94.48896 90.09939 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 89787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44051 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25864 mr = 59211 m= 2386 mr = 16718 m= 50 mr = 954 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 41204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 596 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 33082 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) : 0.5195185 object centre at (A) : 62.49050 49.11900 27.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2439486E-03 -1.0610036E-02 midg,1,midg; midg,igrid,midg 2.2945156E-02 1.6551599E-02 1,midg,midg; igrid,midg,midg -1.4219665E-03 1.2321603E-02 gauss-seidel spectral radius is 0.9981854 estimated iterations to convergence 186 setup time was (sec) 1.020000 now iterating at: 14:05:17 rms-change max change #iterations 3.852729 185.5890 at 10iterations 1.592638 56.37177 at 20iterations 0.6626483 23.53076 at 30iterations 0.2755882 8.711410 at 40iterations 0.1149377 3.986607 at 50iterations 4.7776580E-02 1.434475 at 60iterations 1.9955875E-02 0.6242070 at 70iterations 8.2915295E-03 0.2600174 at 80iterations 3.4713501E-03 0.1173515 at 90iterations 1.4573297E-03 4.9972534E-02 at 100iterations 6.1527325E-04 2.3403168E-02 at 110iterations 2.6668678E-04 8.5010529E-03 at 120iterations finished qdiffx linear iterations at : 14:05:24 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 2.6668678E-04 8.5010529E-03 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 14:05:24 8.136u 0.228s 0:08.75 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 14:05:24 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: SEP 107 has a net charge of -0.4750 !!! WARNING: SEP 739 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.337833 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): 28.22800 96.75300 ymin,ymax (A): 17.48400 80.75400 zmin,zma (A): 0.9569999 54.90500 x,y,z range (A): 68.52499 63.27000 53.94800 scale (grids/A): 2.337833 object centre (A): 62.49050 49.11900 27.93100 number of atom coordinates read : 4549 total number of charged atoms : 4384 net assigned charge : 5.050025 assigned positive charge : 690.8055 centred at (gu) : 86.75621 96.03777 89.77233 assigned negative charge : -685.7604 centred at (gu) : 86.37225 96.73342 90.14890 start vw surface at 0.2500000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 208758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44051 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92291 mr = 146162 m= 23548 mr = 70415 m= 3191 mr = 16463 m= 198 mr = 1893 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 92985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 34979 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) : 1.558555 object centre at (A) : 62.49050 49.11900 27.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9464219E-02 -0.1482148 midg,1,midg; midg,igrid,midg 0.3347095 0.3963858 1,midg,midg; igrid,midg,midg 0.1514355 0.2318664 gauss-seidel spectral radius is 0.9991913 estimated iterations to convergence 278 setup time was (sec) 1.980000 now iterating at: 14:05:26 rms-change max change #iterations 10.51127 343.7216 at 10iterations 6.203896 132.0471 at 20iterations 3.595582 76.65955 at 30iterations 2.070203 44.49896 at 40iterations 1.187009 26.41048 at 50iterations 0.6764839 12.70322 at 60iterations 0.3842561 7.574007 at 70iterations 0.2182047 4.088220 at 80iterations 0.1232831 2.423159 at 90iterations 6.9662288E-02 1.466912 at 100iterations 3.9314091E-02 0.7273159 at 110iterations 2.2131640E-02 0.4114151 at 120iterations 1.2473985E-02 0.2379198 at 130iterations 7.0141256E-03 0.1334057 at 140iterations 3.9558783E-03 7.8615189E-02 at 150iterations 2.2314517E-03 4.0277481E-02 at 160iterations 1.2650132E-03 2.5691986E-02 at 170iterations 7.2232087E-04 1.4406204E-02 at 180iterations finished qdiffx linear iterations at : 14:05:37 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 7.2232087E-04 1.4406204E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 14:05:38 12.707u 0.205s 0:13.26 97.2% 0+0k 0+0io 0pf+0w