Sat Oct 15 12:53:52 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 15 2011 at 12:53:52 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 = 3159 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: 0.5814239 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): -43.17500 18.05400 ymin,ymax (A): -55.13100 0.8600000 zmin,zma (A): -90.83500 -31.43000 x,y,z range (A): 61.22900 55.99100 59.40500 scale (grids/A): 0.5814239 object centre (A): -12.56050 -27.13550 -61.13250 number of atom coordinates read : 3159 total number of charged atoms : 3015 net assigned charge : -3.499981 assigned positive charge : 463.3733 centred at (gu) : 88.79667 91.73081 88.41339 assigned negative charge : -466.8752 centred at (gu) : 88.77532 91.71869 88.50261 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7385 nv = 96 ne = 84 npr = 60529 no. pairs analyzed = 60529 no. exposed pairs = 4511 no. arc points = 33369 no. surface atoms = 1502 nbur = 1657 mkacc time = 0.1000000 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= 359 mr = 3438 m= 4 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3314 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9202 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9088968E-09 -2.0752939E-09 midg,1,midg; midg,igrid,midg -7.5938933E-10 -7.9718793E-10 1,midg,midg; igrid,midg,midg -1.7832259E-09 -2.5029454E-10 gauss-seidel spectral radius is 0.9847718 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 12:53:53 rms-change max change #iterations 9.9028431E-02 16.60925 at 10iterations 7.7602435E-03 1.098423 at 20iterations 6.0595025E-04 8.9087963E-02 at 30iterations 4.9275724E-05 6.7787170E-03 at 40iterations 4.7067178E-06 7.2097778E-04 at 50iterations finished qdiffx linear iterations at : 12:53:56 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 4.7067178E-06 7.2097778E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 12:53:57 3.473u 0.185s 0:04.18 87.3% 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 12:53:57 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 = 3159 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: 1.744272 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): -43.17500 18.05400 ymin,ymax (A): -55.13100 0.8600000 zmin,zma (A): -90.83500 -31.43000 x,y,z range (A): 61.22900 55.99100 59.40500 scale (grids/A): 1.744272 object centre (A): -12.56050 -27.13550 -61.13250 number of atom coordinates read : 3159 total number of charged atoms : 3015 net assigned charge : -3.499981 assigned positive charge : 463.3733 centred at (gu) : 86.38903 95.19133 85.23933 assigned negative charge : -466.8752 centred at (gu) : 86.32574 95.15572 85.50740 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 79651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33369 grid for indexing accessible points = 1.400000 m= 25351 mr = 50281 m= 3543 mr = 16720 m= 139 mr = 1851 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 0.3700000 number of dielectric boundary points 39817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23440 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) : 0.5814239 object centre at (A) : -12.56050 -27.13550 -61.13250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2922241E-02 -2.2781452E-02 midg,1,midg; midg,igrid,midg -1.4170737E-02 -4.0114280E-03 1,midg,midg; igrid,midg,midg -6.6101868E-03 6.5268977E-03 gauss-seidel spectral radius is 0.9984695 estimated iterations to convergence 203 setup time was (sec) 0.6000000 now iterating at: 12:53:58 rms-change max change #iterations 3.917500 198.1086 at 10iterations 1.735268 61.48620 at 20iterations 0.7748922 26.03677 at 30iterations 0.3458064 10.46382 at 40iterations 0.1545506 4.881523 at 50iterations 6.8734176E-02 2.060062 at 60iterations 3.0799935E-02 1.020203 at 70iterations 1.3729852E-02 0.4409237 at 80iterations 6.1559775E-03 0.2315331 at 90iterations 2.7418940E-03 9.2063904E-02 at 100iterations 1.2344099E-03 3.9662302E-02 at 110iterations 5.5011682E-04 2.0355225E-02 at 120iterations finished qdiffx linear iterations at : 12:54:05 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 5.5011682E-04 2.0355225E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 12:54:05 8.024u 0.229s 0:08.53 96.6% 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 12:54:05 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 = 3159 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: 2.616407 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): -43.17500 18.05400 ymin,ymax (A): -55.13100 0.8600000 zmin,zma (A): -90.83500 -31.43000 x,y,z range (A): 61.22900 55.99100 59.40500 scale (grids/A): 2.616407 object centre (A): -12.56050 -27.13550 -61.13250 number of atom coordinates read : 3159 total number of charged atoms : 3015 net assigned charge : -3.499981 assigned positive charge : 463.3733 centred at (gu) : 84.58324 97.78673 82.85879 assigned negative charge : -466.8752 centred at (gu) : 84.48848 97.73357 83.26103 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 184404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33369 grid for indexing accessible points = 1.400000 m= 83572 mr = 123873 m= 27561 mr = 63839 m= 5835 mr = 20306 m= 613 mr = 3934 m= 12 mr = 304 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1268 time to turn everything in is 0.9500000 number of dielectric boundary points 89741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 24112 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) : 1.744272 object centre at (A) : -12.56050 -27.13550 -61.13250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1976229 -0.3743030 midg,1,midg; midg,igrid,midg -0.2491763 -5.6908917E-02 1,midg,midg; igrid,midg,midg -9.8420903E-02 8.9170970E-02 gauss-seidel spectral radius is 0.9992411 estimated iterations to convergence 287 setup time was (sec) 1.180000 now iterating at: 12:54:07 rms-change max change #iterations 9.946960 314.2596 at 10iterations 5.895554 153.1620 at 20iterations 3.441202 82.67991 at 30iterations 2.009015 44.76660 at 40iterations 1.163951 25.02533 at 50iterations 0.6716033 13.26804 at 60iterations 0.3864233 8.333890 at 70iterations 0.2218812 4.640917 at 80iterations 0.1274130 2.489029 at 90iterations 7.2967313E-02 1.300476 at 100iterations 4.1707341E-02 0.7466204 at 110iterations 2.3925068E-02 0.4245415 at 120iterations 1.3655563E-02 0.2491684 at 130iterations 7.7973930E-03 0.1446781 at 140iterations 4.4705262E-03 8.4634781E-02 at 150iterations 2.5423504E-03 4.8698425E-02 at 160iterations 1.4517343E-03 2.6258230E-02 at 170iterations 8.3057722E-04 1.6151428E-02 at 180iterations finished qdiffx linear iterations at : 12:54:18 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 8.3057722E-04 1.6151428E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 12:54:19 12.790u 0.227s 0:13.32 97.6% 0+0k 0+0io 0pf+0w