Tue Oct 11 06:37:42 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 Tue Oct 11 2011 at 06:37:42 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 = 2045 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: 0.7069664 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): -21.07000 24.50000 ymin,ymax (A): -26.78400 10.66700 zmin,zma (A): -14.05700 36.29900 x,y,z range (A): 45.57000 37.45100 50.35600 scale (grids/A): 0.7069664 object centre (A): 1.715000 -8.058500 11.12100 number of atom coordinates read : 2045 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.04399 90.90688 89.42165 assigned negative charge : -305.3172 centred at (gu) : 89.86469 90.89957 89.39640 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6884 nv = 96 ne = 84 npr = 40871 no. pairs analyzed = 40871 no. exposed pairs = 2481 no. arc points = 17242 no. surface atoms = 847 nbur = 1198 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 3926 m= 7 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1563 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6222429E-08 6.6917828E-08 midg,1,midg; midg,igrid,midg 4.9919102E-08 7.8508698E-08 1,midg,midg; igrid,midg,midg -2.4484963E-08 1.4813662E-07 gauss-seidel spectral radius is 0.9895670 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 06:37:43 rms-change max change #iterations 0.1927155 27.69896 at 10iterations 2.4001159E-02 3.843190 at 20iterations 3.0208570E-03 0.4933662 at 30iterations 4.5433964E-04 6.1603546E-02 at 40iterations 9.7424978E-05 1.4881134E-02 at 50iterations finished qdiffx linear iterations at : 06:37:46 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 9.7424978E-05 1.4881134E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 06:37:47 4.073u 0.250s 0:04.67 92.5% 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 Tue Oct 11 2011 at 06:37:47 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 = 2045 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: 2.120899 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): -21.07000 24.50000 ymin,ymax (A): -26.78400 10.66700 zmin,zma (A): -14.05700 36.29900 x,y,z range (A): 45.57000 37.45100 50.35600 scale (grids/A): 2.120899 object centre (A): 1.715000 -8.058500 11.12100 number of atom coordinates read : 2045 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.13195 92.72054 88.26513 assigned negative charge : -305.3172 centred at (gu) : 89.59427 92.69891 88.18931 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17242 grid for indexing accessible points = 1.400000 m= 29266 mr = 52322 m= 5692 mr = 22186 m= 538 mr = 3805 m= 10 mr = 277 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 30659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15388 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) : 0.7069664 object centre at (A) : 1.715000 -8.058500 11.12100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0644753E-02 4.8066098E-02 midg,1,midg; midg,igrid,midg 7.7072820E-03 3.5309903E-02 1,midg,midg; igrid,midg,midg 4.4258237E-03 4.1287653E-02 gauss-seidel spectral radius is 0.9988262 estimated iterations to convergence 231 setup time was (sec) 0.9700000 now iterating at: 06:37:48 rms-change max change #iterations 4.548148 187.5942 at 10iterations 2.244659 74.52544 at 20iterations 1.110393 34.52058 at 30iterations 0.5496859 18.55584 at 40iterations 0.2737083 9.017451 at 50iterations 0.1360305 4.307220 at 60iterations 6.7383155E-02 2.034105 at 70iterations 3.3398017E-02 1.001800 at 80iterations 1.6614009E-02 0.4752197 at 90iterations 8.2788300E-03 0.2548218 at 100iterations 4.1345744E-03 0.1311493 at 110iterations 2.0876199E-03 6.2380791E-02 at 120iterations finished qdiffx linear iterations at : 06:37:57 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 2.0876199E-03 6.2380791E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 06:37:57 9.526u 0.321s 0:10.22 96.2% 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 Tue Oct 11 2011 at 06:37:57 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 = 2045 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: 3.181349 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): -21.07000 24.50000 ymin,ymax (A): -26.78400 10.66700 zmin,zma (A): -14.05700 36.29900 x,y,z range (A): 45.57000 37.45100 50.35600 scale (grids/A): 3.181349 object centre (A): 1.715000 -8.058500 11.12100 number of atom coordinates read : 2045 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.19785 94.08089 87.39778 assigned negative charge : -305.3172 centred at (gu) : 89.39143 94.04839 87.28405 start vw surface at 0.1400000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 170023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17242 grid for indexing accessible points = 1.400000 m= 91721 mr = 125880 m= 37113 mr = 76472 m= 10748 mr = 30367 m= 2157 mr = 8333 m= 232 mr = 1578 m= 3 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.160000 number of dielectric boundary points 69223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 15496 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) : 2.120899 object centre at (A) : 1.715000 -8.058500 11.12100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5773821 0.4420953 midg,1,midg; midg,igrid,midg 4.5458104E-02 0.2877618 1,midg,midg; igrid,midg,midg 0.1134868 0.3278753 gauss-seidel spectral radius is 0.9992945 estimated iterations to convergence 297 setup time was (sec) 2.490000 now iterating at: 06:38:00 rms-change max change #iterations 10.21728 443.4193 at 10iterations 6.032821 138.9526 at 20iterations 3.561433 71.72583 at 30iterations 2.102756 40.00001 at 40iterations 1.236213 25.32597 at 50iterations 0.7256273 16.93710 at 60iterations 0.4252943 8.919861 at 70iterations 0.2496123 4.547714 at 80iterations 0.1463575 2.492424 at 90iterations 8.5612096E-02 1.475546 at 100iterations 5.0195746E-02 0.8949871 at 110iterations 2.9538104E-02 0.5008850 at 120iterations 1.7379804E-02 0.3240285 at 130iterations 1.0341661E-02 0.2051733 at 140iterations 6.2232921E-03 0.1205425 at 150iterations 3.8413913E-03 6.9122314E-02 at 160iterations 2.4647193E-03 4.5415878E-02 at 170iterations 1.6661936E-03 3.1871796E-02 at 180iterations finished qdiffx linear iterations at : 06:38:14 total time elapsed so far: 16.23000 # loops : 180 mean,max change (kT/e) : 1.6661936E-03 3.1871796E-02 energy calculations done at 16.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.41000 DelPhi exited at 06:38:15 16.407u 0.296s 0:17.39 95.9% 0+0k 0+0io 0pf+0w