Mon Oct 10 00:02:36 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 Mon Oct 10 2011 at 00:02:36 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 = 2570 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: 0.6211506 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): -7.854000 49.45900 ymin,ymax (A): -27.35200 22.85700 zmin,zma (A): -7.570000 40.40900 x,y,z range (A): 57.31300 50.20900 47.97900 scale (grids/A): 0.6211506 object centre (A): 20.80250 -2.247499 16.41950 number of atom coordinates read : 2570 total number of charged atoms : 2431 net assigned charge : 3.000007 assigned positive charge : 388.5539 centred at (gu) : 89.70995 90.82186 87.92989 assigned negative charge : -385.5547 centred at (gu) : 89.59832 90.88766 87.92042 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6442 nv = 96 ne = 84 npr = 52640 no. pairs analyzed = 52640 no. exposed pairs = 3172 no. arc points = 22205 no. surface atoms = 1070 nbur = 1500 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 268 mr = 3450 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.1900000 number of dielectric boundary points 3244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2270 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9912279E-09 2.0723541E-09 midg,1,midg; midg,igrid,midg 5.8548495E-09 -2.3465760E-09 1,midg,midg; igrid,midg,midg -5.4514659E-09 9.4341832E-09 gauss-seidel spectral radius is 0.9865727 estimated iterations to convergence 71 setup time was (sec) 0.3800000 now iterating at: 00:02:37 rms-change max change #iterations 0.1254080 17.70378 at 10iterations 1.1405559E-02 1.712765 at 20iterations 1.0523222E-03 0.1501694 at 30iterations 9.8289609E-05 1.3507843E-02 at 40iterations 8.9560799E-06 1.3160706E-03 at 50iterations finished qdiffx linear iterations at : 00:02:40 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 8.9560799E-06 1.3160706E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 00:02:40 3.428u 0.175s 0:03.88 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 Mon Oct 10 2011 at 00:02:40 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 = 2570 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: 1.863452 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): -7.854000 49.45900 ymin,ymax (A): -27.35200 22.85700 zmin,zma (A): -7.570000 40.40900 x,y,z range (A): 57.31300 50.20900 47.97900 scale (grids/A): 1.863452 object centre (A): 20.80250 -2.247499 16.41950 number of atom coordinates read : 2570 total number of charged atoms : 2431 net assigned charge : 3.000007 assigned positive charge : 388.5539 centred at (gu) : 89.12917 92.46538 83.78907 assigned negative charge : -385.5547 centred at (gu) : 88.79479 92.66282 83.76114 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22205 grid for indexing accessible points = 1.400000 m= 22805 mr = 47826 m= 2787 mr = 16413 m= 111 mr = 1618 m= 0 mr = 37 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 489 time to turn everything in is 0.3500000 number of dielectric boundary points 30041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19046 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) : 0.6211506 object centre at (A) : 20.80250 -2.247499 16.41950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5109328E-02 1.6006851E-03 midg,1,midg; midg,igrid,midg 8.8202534E-03 3.8716481E-03 1,midg,midg; igrid,midg,midg -2.5812006E-02 3.6737472E-02 gauss-seidel spectral radius is 0.9985645 estimated iterations to convergence 209 setup time was (sec) 0.5600000 now iterating at: 00:02:41 rms-change max change #iterations 4.017318 174.5227 at 10iterations 1.835591 67.73434 at 20iterations 0.8421608 28.53657 at 30iterations 0.3852588 14.58715 at 40iterations 0.1775111 5.488348 at 50iterations 8.1397168E-02 2.641995 at 60iterations 3.7298378E-02 1.237846 at 70iterations 1.7133227E-02 0.5422668 at 80iterations 7.8555951E-03 0.2598381 at 90iterations 3.6150254E-03 0.1167307 at 100iterations 1.6603229E-03 5.4816246E-02 at 110iterations 7.5927767E-04 2.8565049E-02 at 120iterations finished qdiffx linear iterations at : 00:02:48 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 7.5927767E-04 2.8565049E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 00:02:48 7.824u 0.202s 0:08.31 96.5% 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 Mon Oct 10 2011 at 00:02:48 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 = 2570 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: 2.795177 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): -7.854000 49.45900 ymin,ymax (A): -27.35200 22.85700 zmin,zma (A): -7.570000 40.40900 x,y,z range (A): 57.31300 50.20900 47.97900 scale (grids/A): 2.795177 object centre (A): 20.80250 -2.247499 16.41950 number of atom coordinates read : 2570 total number of charged atoms : 2431 net assigned charge : 3.000007 assigned positive charge : 388.5539 centred at (gu) : 88.69363 93.69784 80.68359 assigned negative charge : -385.5547 centred at (gu) : 88.19206 93.99432 80.64159 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22205 grid for indexing accessible points = 1.400000 m= 76729 mr = 116460 m= 24589 mr = 61973 m= 4698 mr = 19444 m= 491 mr = 3411 m= 23 mr = 297 m= 0 mr = 12 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 1609 time to turn everything in is 0.8800000 number of dielectric boundary points 67682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 19447 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) : 1.863452 object centre at (A) : 20.80250 -2.247499 16.41950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1593823 1.8147515E-02 midg,1,midg; midg,igrid,midg 8.7772861E-02 0.1307926 1,midg,midg; igrid,midg,midg -0.3214335 0.4598893 gauss-seidel spectral radius is 0.9992426 estimated iterations to convergence 287 setup time was (sec) 1.110000 now iterating at: 00:02:50 rms-change max change #iterations 9.456423 350.4733 at 10iterations 5.438147 120.0401 at 20iterations 3.101297 62.92999 at 30iterations 1.769054 36.29719 at 40iterations 1.009699 20.71749 at 50iterations 0.5746871 10.89923 at 60iterations 0.3267385 6.383776 at 70iterations 0.1859176 3.760214 at 80iterations 0.1060003 2.077246 at 90iterations 6.0178831E-02 1.147215 at 100iterations 3.4354672E-02 0.6879997 at 110iterations 1.9541221E-02 0.3539524 at 120iterations 1.1140663E-02 0.2113400 at 130iterations 6.3393721E-03 0.1221313 at 140iterations 3.6061958E-03 6.8671703E-02 at 150iterations 2.0542506E-03 3.7812233E-02 at 160iterations 1.1706336E-03 2.3729801E-02 at 170iterations 6.6507293E-04 1.1463284E-02 at 180iterations finished qdiffx linear iterations at : 00:03:01 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 6.6507293E-04 1.1463284E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 00:03:02 12.638u 0.206s 0:13.12 97.7% 0+0k 0+0io 0pf+0w