Mon Oct 10 17:03:27 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 Mon Oct 10 2011 at 17:03:27 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3460 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6196045 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): 12.37100 62.61900 ymin,ymax (A): -40.93400 10.31400 zmin,zma (A): 28.45700 85.91300 x,y,z range (A): 50.24800 51.24800 57.45600 scale (grids/A): 0.6196045 object centre (A): 37.49500 -15.31000 57.18500 number of atom coordinates read : 3460 total number of charged atoms : 3311 net assigned charge : 3.000040 assigned positive charge : 531.2594 centred at (gu) : 89.48526 90.90572 89.61260 assigned negative charge : -528.2607 centred at (gu) : 89.51331 90.86869 89.67205 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8679 nv = 96 ne = 84 npr = 71379 no. pairs analyzed = 71379 no. exposed pairs = 3851 no. arc points = 26474 no. surface atoms = 1298 nbur = 2162 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 519 mr = 5168 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4400000 number of dielectric boundary points 3963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2792 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10953 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2738447E-09 -2.7729423E-09 midg,1,midg; midg,igrid,midg -8.0398460E-10 6.8545405E-09 1,midg,midg; igrid,midg,midg 5.3904925E-09 -1.6637196E-10 gauss-seidel spectral radius is 0.9865732 estimated iterations to convergence 71 setup time was (sec) 0.7900000 now iterating at: 17:03:28 rms-change max change #iterations 0.1524636 22.01443 at 10iterations 1.4433559E-02 1.817110 at 20iterations 1.8439493E-03 0.2373276 at 30iterations 5.9589883E-04 8.3850861E-02 at 40iterations 2.7083189E-04 3.5820007E-02 at 50iterations finished qdiffx linear iterations at : 17:03:33 total time elapsed so far: 5.150000 # loops : 50 mean,max change (kT/e) : 2.7083189E-04 3.5820007E-02 energy calculations done at 5.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.340000 DelPhi exited at 17:03:34 5.343u 0.413s 0:06.44 89.2% 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 Mon Oct 10 2011 at 17:03:34 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3460 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.858814 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): 12.37100 62.61900 ymin,ymax (A): -40.93400 10.31400 zmin,zma (A): 28.45700 85.91300 x,y,z range (A): 50.24800 51.24800 57.45600 scale (grids/A): 1.858814 object centre (A): 37.49500 -15.31000 57.18500 number of atom coordinates read : 3460 total number of charged atoms : 3311 net assigned charge : 3.000040 assigned positive charge : 531.2594 centred at (gu) : 88.45473 92.71619 88.83692 assigned negative charge : -528.2607 centred at (gu) : 88.53943 92.60565 89.01537 start vw surface at 0.1800000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 94422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 35886 mr = 68639 m= 5629 mr = 27334 m= 325 mr = 3498 m= 4 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2962 time to turn everything in is 0.8600000 number of dielectric boundary points 36666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 25964 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) : 0.6196045 object centre at (A) : 37.49500 -15.31000 57.18500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8927703E-03 -1.3693980E-02 midg,1,midg; midg,igrid,midg 3.3824474E-03 1.8356843E-02 1,midg,midg; igrid,midg,midg 1.0066960E-02 3.1283960E-02 gauss-seidel spectral radius is 0.9986418 estimated iterations to convergence 215 setup time was (sec) 1.210000 now iterating at: 17:03:35 rms-change max change #iterations 4.831793 185.4164 at 10iterations 2.279341 65.82944 at 20iterations 1.072381 29.72246 at 30iterations 0.5048921 13.68250 at 40iterations 0.2385012 6.371540 at 50iterations 0.1122550 3.092480 at 60iterations 5.2833084E-02 1.515721 at 70iterations 2.5012629E-02 0.6814861 at 80iterations 1.1916432E-02 0.3275681 at 90iterations 5.7255290E-03 0.1720986 at 100iterations 2.8697576E-03 8.4947109E-02 at 110iterations 1.5563510E-03 4.3605804E-02 at 120iterations finished qdiffx linear iterations at : 17:03:46 total time elapsed so far: 11.71000 # loops : 120 mean,max change (kT/e) : 1.5563510E-03 4.3605804E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 17:03:47 11.904u 0.561s 0:13.11 95.0% 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 Mon Oct 10 2011 at 17:03:47 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3460 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.788220 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): 12.37100 62.61900 ymin,ymax (A): -40.93400 10.31400 zmin,zma (A): 28.45700 85.91300 x,y,z range (A): 50.24800 51.24800 57.45600 scale (grids/A): 2.788220 object centre (A): 37.49500 -15.31000 57.18500 number of atom coordinates read : 3460 total number of charged atoms : 3311 net assigned charge : 3.000040 assigned positive charge : 531.2594 centred at (gu) : 87.68181 94.07420 88.25512 assigned negative charge : -528.2607 centred at (gu) : 87.80901 93.90826 88.52302 start vw surface at 0.1900000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 218698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 116014 mr = 165799 m= 42310 mr = 96813 m= 9891 mr = 34586 m= 1336 mr = 7400 m= 79 mr = 885 m= 0 mr = 30 time to grow re-entrant surface = 1.400000 no. cavity mid-points inaccessible to solvent = 10343 time to turn everything in is 2.280000 number of dielectric boundary points 82815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.470000 number of grid points assigned charge 26486 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) : 1.858814 object centre at (A) : 37.49500 -15.31000 57.18500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1531888 -8.4203742E-02 midg,1,midg; midg,igrid,midg -1.0123991E-02 0.2769115 1,midg,midg; igrid,midg,midg 0.1363130 0.4786341 gauss-seidel spectral radius is 0.9992675 estimated iterations to convergence 292 setup time was (sec) 2.730000 now iterating at: 17:03:50 rms-change max change #iterations 11.30688 285.6626 at 10iterations 6.676421 136.8631 at 20iterations 3.913896 83.30490 at 30iterations 2.292291 43.09650 at 40iterations 1.337070 24.71841 at 50iterations 0.7772517 14.55447 at 60iterations 0.4520915 7.828640 at 70iterations 0.2626073 4.582613 at 80iterations 0.1523021 2.913871 at 90iterations 8.8176988E-02 1.606989 at 100iterations 5.1218260E-02 0.8853884 at 110iterations 2.9662540E-02 0.5396996 at 120iterations 1.7267579E-02 0.2822657 at 130iterations 1.0046338E-02 0.1626396 at 140iterations 5.8880686E-03 9.3510628E-02 at 150iterations 3.4981882E-03 6.2902451E-02 at 160iterations 2.1396850E-03 3.8808823E-02 at 170iterations 1.3765888E-03 2.3633957E-02 at 180iterations finished qdiffx linear iterations at : 17:04:08 total time elapsed so far: 20.76000 # loops : 180 mean,max change (kT/e) : 1.3765888E-03 2.3633957E-02 energy calculations done at 20.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.94000 DelPhi exited at 17:04:09 20.939u 0.576s 0:22.53 95.4% 0+0k 0+0io 0pf+0w