Sat Oct 15 14:32:54 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 Sat Oct 15 2011 at 14:32:54 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3008 !!! WARNING: HIT 111 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5918143 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): -8.964000 51.19000 ymin,ymax (A): -7.984000 39.92700 zmin,zma (A): -3.541000 53.35200 x,y,z range (A): 60.15400 47.91100 56.89300 scale (grids/A): 0.5918143 object centre (A): 21.11300 15.97150 24.90550 number of atom coordinates read : 3008 total number of charged atoms : 2866 net assigned charge : -3.485963 assigned positive charge : 457.0949 centred at (gu) : 89.24951 89.61635 89.37053 assigned negative charge : -460.5821 centred at (gu) : 89.16077 89.52159 89.28554 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6969 nv = 96 ne = 84 npr = 60162 no. pairs analyzed = 60162 no. exposed pairs = 3937 no. arc points = 27861 no. surface atoms = 1344 nbur = 1664 mkacc time = 9.9999994E-02 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 = 1.484000 m= 317 mr = 3580 m= 0 mr = 16 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2300000 number of dielectric boundary points 3690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5680149E-09 1.4944657E-09 midg,1,midg; midg,igrid,midg -4.6795043E-09 1.8779327E-09 1,midg,midg; igrid,midg,midg -4.8511257E-09 1.5548428E-09 gauss-seidel spectral radius is 0.9852657 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 14:32:55 rms-change max change #iterations 0.1119098 17.19006 at 10iterations 9.1985362E-03 1.346397 at 20iterations 7.5962965E-04 0.1097307 at 30iterations 6.4379543E-05 9.5891953E-03 at 40iterations 5.8045098E-06 8.9263916E-04 at 50iterations finished qdiffx linear iterations at : 14:33:00 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 5.8045098E-06 8.9263916E-04 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 14:33:00 3.606u 0.189s 0:06.29 60.0% 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 15 2011 at 14:33:00 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3008 !!! WARNING: HIT 111 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.775443 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): -8.964000 51.19000 ymin,ymax (A): -7.984000 39.92700 zmin,zma (A): -3.541000 53.35200 x,y,z range (A): 60.15400 47.91100 56.89300 scale (grids/A): 1.775443 object centre (A): 21.11300 15.97150 24.90550 number of atom coordinates read : 3008 total number of charged atoms : 2866 net assigned charge : -3.485963 assigned positive charge : 457.0949 centred at (gu) : 87.74791 88.84845 88.11090 assigned negative charge : -460.5821 centred at (gu) : 87.48199 88.56438 87.85635 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75283 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27861 grid for indexing accessible points = 1.400000 m= 25230 mr = 50277 m= 3388 mr = 17814 m= 155 mr = 1811 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 0.3800000 number of dielectric boundary points 34120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 22326 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) : 0.5918143 object centre at (A) : 21.11300 15.97150 24.90550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4461851E-03 9.3172034E-03 midg,1,midg; midg,igrid,midg -2.1065034E-02 -8.1763003E-04 1,midg,midg; igrid,midg,midg -3.9978061E-02 2.5295787E-02 gauss-seidel spectral radius is 0.9984794 estimated iterations to convergence 203 setup time was (sec) 0.6100000 now iterating at: 14:33:01 rms-change max change #iterations 4.041413 182.1973 at 10iterations 1.797939 76.97613 at 20iterations 0.8063509 31.28865 at 30iterations 0.3631055 12.06017 at 40iterations 0.1619453 5.357925 at 50iterations 7.2617777E-02 2.422844 at 60iterations 3.2668415E-02 1.118579 at 70iterations 1.4633050E-02 0.5704803 at 80iterations 6.5845945E-03 0.2086344 at 90iterations 2.9475116E-03 9.5739365E-02 at 100iterations 1.3215677E-03 4.4529915E-02 at 110iterations 5.9451599E-04 1.9878387E-02 at 120iterations finished qdiffx linear iterations at : 14:33:09 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 5.9451599E-04 1.9878387E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 14:33:10 8.186u 0.254s 0:09.34 90.2% 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 Sat Oct 15 2011 at 14:33:10 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3008 !!! WARNING: HIT 111 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.663164 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): -8.964000 51.19000 ymin,ymax (A): -7.984000 39.92700 zmin,zma (A): -3.541000 53.35200 x,y,z range (A): 60.15400 47.91100 56.89300 scale (grids/A): 2.663164 object centre (A): 21.11300 15.97150 24.90550 number of atom coordinates read : 3008 total number of charged atoms : 2866 net assigned charge : -3.485963 assigned positive charge : 457.0949 centred at (gu) : 86.62160 88.27237 87.16604 assigned negative charge : -460.5821 centred at (gu) : 86.22290 87.84623 86.78448 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 174450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27861 grid for indexing accessible points = 1.400000 m= 83441 mr = 122835 m= 27641 mr = 66390 m= 5684 mr = 21340 m= 612 mr = 3954 m= 33 mr = 339 m= 0 mr = 4 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1912 time to turn everything in is 1.000000 number of dielectric boundary points 76999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 22924 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) : 1.775443 object centre at (A) : 21.11300 15.97150 24.90550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1589859 7.4830003E-02 midg,1,midg; midg,igrid,midg -0.2626130 1.6950525E-02 1,midg,midg; igrid,midg,midg -0.5567111 0.3723367 gauss-seidel spectral radius is 0.9992343 estimated iterations to convergence 285 setup time was (sec) 1.290000 now iterating at: 14:33:11 rms-change max change #iterations 10.06240 333.6049 at 10iterations 5.876618 130.2225 at 20iterations 3.406153 69.25718 at 30iterations 1.963119 43.09265 at 40iterations 1.128697 23.28588 at 50iterations 0.6474020 12.75695 at 60iterations 0.3696291 7.036198 at 70iterations 0.2111672 3.827831 at 80iterations 0.1203993 2.211162 at 90iterations 6.8671159E-02 1.253895 at 100iterations 3.9106183E-02 0.7455406 at 110iterations 2.2273775E-02 0.4448242 at 120iterations 1.2663651E-02 0.2563400 at 130iterations 7.2240811E-03 0.1297417 at 140iterations 4.1086595E-03 9.3711853E-02 at 150iterations 2.3391396E-03 4.1191101E-02 at 160iterations 1.3284539E-03 2.3139954E-02 at 170iterations 7.5587601E-04 1.4714241E-02 at 180iterations finished qdiffx linear iterations at : 14:33:24 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 7.5587601E-04 1.4714241E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 14:33:24 13.158u 0.293s 0:14.27 94.1% 0+0k 0+0io 0pf+0w