Sat Oct 8 11:34:37 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 Sat Oct 8 2011 at 11:34:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5708055 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 0.5708055 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 91.99503 88.65961 88.47491 assigned negative charge : -273.8725 centred at (gu) : 91.99344 88.66325 88.66789 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4527 nv = 96 ne = 84 npr = 43500 no. pairs analyzed = 43500 no. exposed pairs = 2710 no. arc points = 19357 no. surface atoms = 919 nbur = 1135 mkacc time = 0.1200000 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 = 1.540000 m= 227 mr = 2177 m= 0 mr = 18 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2900000 number of dielectric boundary points 2559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1876 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2052158E-09 -1.5937788E-09 midg,1,midg; midg,igrid,midg -4.2065462E-10 -2.7916472E-10 1,midg,midg; igrid,midg,midg -2.2794613E-10 -5.2343191E-10 gauss-seidel spectral radius is 0.9840972 estimated iterations to convergence 65 setup time was (sec) 0.5600000 now iterating at: 11:34:38 rms-change max change #iterations 6.7894921E-02 13.89122 at 10iterations 5.8259913E-03 1.010594 at 20iterations 1.2887625E-03 0.2640324 at 30iterations 5.4100668E-04 0.1129112 at 40iterations 2.3588345E-04 4.9358368E-02 at 50iterations finished qdiffx linear iterations at : 11:34:41 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 2.3588345E-04 4.9358368E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 11:34:42 4.029u 0.252s 0:04.63 92.2% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 11:34:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.712417 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 1.712417 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 95.98523 85.97900 85.42516 assigned negative charge : -273.8725 centred at (gu) : 95.98069 85.99010 86.00386 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 49311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19357 grid for indexing accessible points = 1.400000 m= 15508 mr = 31782 m= 2001 mr = 10448 m= 45 mr = 1043 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 850 time to turn everything in is 0.4700000 number of dielectric boundary points 23589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14997 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) : 0.5708055 object centre at (A) : -9.177502 -6.357000 49.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6554432E-02 -1.0796237E-02 midg,1,midg; midg,igrid,midg -2.9648207E-03 -1.0081131E-03 1,midg,midg; igrid,midg,midg -3.2753168E-04 -5.7483069E-04 gauss-seidel spectral radius is 0.9982592 estimated iterations to convergence 190 setup time was (sec) 0.7600000 now iterating at: 11:34:43 rms-change max change #iterations 2.767957 176.9728 at 10iterations 1.172076 55.01425 at 20iterations 0.4949246 22.14502 at 30iterations 0.2114653 8.663551 at 40iterations 8.9877032E-02 3.390110 at 50iterations 3.8459152E-02 1.520630 at 60iterations 1.6582292E-02 0.6965446 at 70iterations 7.5826240E-03 0.3575554 at 80iterations 3.8486787E-03 0.1825314 at 90iterations 2.2892044E-03 0.1068153 at 100iterations 1.5667832E-03 7.0106506E-02 at 110iterations 1.1552119E-03 5.0430298E-02 at 120iterations finished qdiffx linear iterations at : 11:34:51 total time elapsed so far: 8.920000 # loops : 120 mean,max change (kT/e) : 1.1552119E-03 5.0430298E-02 energy calculations done at 8.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.100000 DelPhi exited at 11:34:52 9.105u 0.281s 0:09.76 96.1% 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 Sat Oct 8 2011 at 11:34:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.568625 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 2.568625 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 98.97779 83.96842 83.13780 assigned negative charge : -273.8725 centred at (gu) : 98.97121 83.98528 84.00581 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 114376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19357 grid for indexing accessible points = 1.400000 m= 51574 mr = 78471 m= 16622 mr = 39632 m= 3189 mr = 12383 m= 238 mr = 2172 m= 2 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 3060 time to turn everything in is 1.100000 number of dielectric boundary points 53220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 15408 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) : 1.712417 object centre at (A) : -9.177502 -6.357000 49.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3196055 -0.1550862 midg,1,midg; midg,igrid,midg -4.2374361E-02 -3.7099912E-03 1,midg,midg; igrid,midg,midg -4.0174765E-03 -1.3689902E-02 gauss-seidel spectral radius is 0.9991370 estimated iterations to convergence 269 setup time was (sec) 1.410000 now iterating at: 11:34:53 rms-change max change #iterations 7.006505 337.7671 at 10iterations 3.927662 107.0389 at 20iterations 2.181163 52.59391 at 30iterations 1.211898 30.23777 at 40iterations 0.6749083 16.28746 at 50iterations 0.3722686 9.013566 at 60iterations 0.2064011 5.930096 at 70iterations 0.1136484 2.652988 at 80iterations 6.2689409E-02 1.788696 at 90iterations 3.4662865E-02 0.7920808 at 100iterations 1.9079989E-02 0.4629440 at 110iterations 1.0567556E-02 0.2478447 at 120iterations 5.9099742E-03 0.1552277 at 130iterations 3.3672201E-03 8.1085205E-02 at 140iterations 1.9914147E-03 5.3039551E-02 at 150iterations 1.2588747E-03 3.4349442E-02 at 160iterations 8.7254768E-04 2.5726318E-02 at 170iterations 6.6170999E-04 1.7412186E-02 at 180iterations finished qdiffx linear iterations at : 11:35:06 total time elapsed so far: 14.50000 # loops : 180 mean,max change (kT/e) : 6.6170999E-04 1.7412186E-02 energy calculations done at 14.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.68000 DelPhi exited at 11:35:07 14.677u 0.298s 0:15.56 96.1% 0+0k 0+0io 0pf+0w