Mon Oct 10 17:04:33 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 17:04:33 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 = 3667 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5206581 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): -17.41100 50.96400 ymin,ymax (A): -27.45600 29.10000 zmin,zma (A): -22.60400 38.13100 x,y,z range (A): 68.37500 56.55600 60.73500 scale (grids/A): 0.5206581 object centre (A): 16.77650 0.8220005 7.763498 number of atom coordinates read : 3667 total number of charged atoms : 3520 net assigned charge : 3.7431717E-05 assigned positive charge : 559.3216 centred at (gu) : 90.04115 88.13210 88.61876 assigned negative charge : -559.3237 centred at (gu) : 90.00899 87.97332 88.63665 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6468 nv = 96 ne = 84 npr = 69808 no. pairs analyzed = 69808 no. exposed pairs = 5103 no. arc points = 37305 no. surface atoms = 1707 nbur = 1960 mkacc time = 0.1800000 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 = 1.652000 m= 239 mr = 2958 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3693 ## 580 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8637 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3212632E-11 -3.1639344E-11 midg,1,midg; midg,igrid,midg -8.0345292E-10 3.0029046E-10 1,midg,midg; igrid,midg,midg -8.8571664E-11 1.0939119E-10 gauss-seidel spectral radius is 0.9810684 estimated iterations to convergence 60 setup time was (sec) 0.6400000 now iterating at: 17:04:34 rms-change max change #iterations 6.2570862E-02 13.68896 at 10iterations 3.5884983E-03 0.7875366 at 20iterations 2.1430447E-04 4.4937134E-02 at 30iterations 1.3224208E-05 2.8686523E-03 at 40iterations 9.1557428E-07 1.6784668E-04 at 50iterations finished qdiffx linear iterations at : 17:04:38 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 9.1557428E-07 1.6784668E-04 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 17:04:38 4.547u 0.393s 0:05.40 91.2% 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 Mon Oct 10 2011 at 17:04:38 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 = 3667 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.561974 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): -17.41100 50.96400 ymin,ymax (A): -27.45600 29.10000 zmin,zma (A): -22.60400 38.13100 x,y,z range (A): 68.37500 56.55600 60.73500 scale (grids/A): 1.561974 object centre (A): 16.77650 0.8220005 7.763498 number of atom coordinates read : 3667 total number of charged atoms : 3520 net assigned charge : 3.7431717E-05 assigned positive charge : 559.3216 centred at (gu) : 90.12218 84.39503 85.85510 assigned negative charge : -559.3237 centred at (gu) : 90.02651 83.91988 85.90948 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37305 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19074 mr = 45421 m= 1466 mr = 11715 m= 25 mr = 494 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1365 time to turn everything in is 0.5800000 number of dielectric boundary points 34905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 519 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 26542 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) : 0.5206581 object centre at (A) : 16.77650 0.8220005 7.763498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5589895E-02 3.1939265E-03 midg,1,midg; midg,igrid,midg -6.9390112E-03 4.2479457E-03 1,midg,midg; igrid,midg,midg -2.5996605E-02 -1.3177311E-02 gauss-seidel spectral radius is 0.9980965 estimated iterations to convergence 182 setup time was (sec) 0.8800000 now iterating at: 17:04:40 rms-change max change #iterations 3.406718 163.8546 at 10iterations 1.381762 53.84071 at 20iterations 0.5618903 23.19962 at 30iterations 0.2282757 9.151157 at 40iterations 9.2830397E-02 3.230049 at 50iterations 3.7939236E-02 1.501668 at 60iterations 1.5481487E-02 0.6003656 at 70iterations 6.3290866E-03 0.2165504 at 80iterations 2.5708776E-03 8.9470789E-02 at 90iterations 1.0490259E-03 3.6240578E-02 at 100iterations 4.2847256E-04 1.5854836E-02 at 110iterations 1.7399805E-04 6.1821938E-03 at 120iterations finished qdiffx linear iterations at : 17:04:49 total time elapsed so far: 10.36000 # loops : 120 mean,max change (kT/e) : 1.7399805E-04 6.1821938E-03 energy calculations done at 10.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 17:04:50 10.569u 0.461s 0:11.42 96.4% 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 17:04:50 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 = 3667 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.342962 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): -17.41100 50.96400 ymin,ymax (A): -27.45600 29.10000 zmin,zma (A): -22.60400 38.13100 x,y,z range (A): 68.37500 56.55600 60.73500 scale (grids/A): 2.342962 object centre (A): 16.77650 0.8220005 7.763498 number of atom coordinates read : 3667 total number of charged atoms : 3520 net assigned charge : 3.7431717E-05 assigned positive charge : 559.3216 centred at (gu) : 90.18296 81.59227 83.78253 assigned negative charge : -559.3237 centred at (gu) : 90.03963 80.87968 83.86411 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37305 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 68348 mr = 112583 m= 16193 mr = 50785 m= 1825 mr = 10923 m= 79 mr = 949 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 4170 time to turn everything in is 1.420000 number of dielectric boundary points 78801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 28098 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) : 1.561974 object centre at (A) : 16.77650 0.8220005 7.763498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2749383 5.2654475E-02 midg,1,midg; midg,igrid,midg -6.2532663E-02 3.4062658E-02 1,midg,midg; igrid,midg,midg -0.6235059 -0.5068186 gauss-seidel spectral radius is 0.9991350 estimated iterations to convergence 269 setup time was (sec) 1.750000 now iterating at: 17:04:52 rms-change max change #iterations 9.197873 311.5842 at 10iterations 5.208039 181.4442 at 20iterations 2.914045 82.87381 at 30iterations 1.620488 36.78479 at 40iterations 0.8994924 20.85418 at 50iterations 0.4984330 11.05997 at 60iterations 0.2749513 5.792698 at 70iterations 0.1515159 3.048906 at 80iterations 8.3344683E-02 2.055084 at 90iterations 4.5827478E-02 1.066402 at 100iterations 2.5181634E-02 0.5074654 at 110iterations 1.3825189E-02 0.3088684 at 120iterations 7.5965389E-03 0.1469975 at 130iterations 4.1557290E-03 8.8520050E-02 at 140iterations 2.2847930E-03 4.8713684E-02 at 150iterations 1.2559539E-03 2.4696350E-02 at 160iterations 6.8827765E-04 1.3604164E-02 at 170iterations 3.7755381E-04 8.1872940E-03 at 180iterations finished qdiffx linear iterations at : 17:05:08 total time elapsed so far: 17.67000 # loops : 180 mean,max change (kT/e) : 3.7755381E-04 8.1872940E-03 energy calculations done at 17.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.82000 DelPhi exited at 17:05:09 17.826u 0.469s 0:18.67 97.9% 0+0k 0+0io 0pf+0w