Sat Oct 15 12:54:43 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 12:54:43 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 = 2906 !!! WARNING: CME 304 has a net charge of -0.3480 !!! WARNING: CME 446 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5797762 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): -22.36700 39.03600 ymin,ymax (A): -25.02600 29.29400 zmin,zma (A): -30.21500 27.37000 x,y,z range (A): 61.40300 54.32000 57.58500 scale (grids/A): 0.5797762 object centre (A): 8.334499 2.134001 -1.422500 number of atom coordinates read : 2906 total number of charged atoms : 2783 net assigned charge : 0.6990355 assigned positive charge : 426.8130 centred at (gu) : 89.57034 89.58171 91.60416 assigned negative charge : -426.1158 centred at (gu) : 89.59122 89.63358 91.60216 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6730 nv = 96 ne = 84 npr = 56612 no. pairs analyzed = 56612 no. exposed pairs = 4082 no. arc points = 29153 no. surface atoms = 1352 nbur = 1554 mkacc time = 0.1300000 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= 340 mr = 3299 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3100000 number of dielectric boundary points 3746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2849 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8418 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1328547E-11 2.6783353E-10 midg,1,midg; midg,igrid,midg 1.3474416E-09 -8.5667867E-10 1,midg,midg; igrid,midg,midg 6.3999378E-10 -2.6485319E-10 gauss-seidel spectral radius is 0.9846559 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 12:54:44 rms-change max change #iterations 9.4895892E-02 15.18881 at 10iterations 7.8690955E-03 1.350128 at 20iterations 1.0687811E-03 0.1841927 at 30iterations 2.8695312E-04 5.3573608E-02 at 40iterations 8.7782413E-05 1.6542435E-02 at 50iterations finished qdiffx linear iterations at : 12:54:48 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 8.7782413E-05 1.6542435E-02 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 12:54:48 4.317u 0.288s 0:04.89 93.8% 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 12:54:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2906 !!! WARNING: CME 304 has a net charge of -0.3480 !!! WARNING: CME 446 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 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: 1.739329 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): -22.36700 39.03600 ymin,ymax (A): -25.02600 29.29400 zmin,zma (A): -30.21500 27.37000 x,y,z range (A): 61.40300 54.32000 57.58500 scale (grids/A): 1.739329 object centre (A): 8.334499 2.134001 -1.422500 number of atom coordinates read : 2906 total number of charged atoms : 2783 net assigned charge : 0.6990355 assigned positive charge : 426.8130 centred at (gu) : 88.71024 88.74415 94.81142 assigned negative charge : -426.1158 centred at (gu) : 88.77341 88.90089 94.80641 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 73452 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29153 grid for indexing accessible points = 1.400000 m= 23763 mr = 48223 m= 3289 mr = 15929 m= 136 mr = 1748 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1382 time to turn everything in is 0.6400000 number of dielectric boundary points 34723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 21672 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) : 0.5797762 object centre at (A) : 8.334499 2.134001 -1.422500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7757933E-03 1.9821608E-03 midg,1,midg; midg,igrid,midg 1.1604908E-02 7.0787850E-03 1,midg,midg; igrid,midg,midg 8.6681182E-03 -2.8519988E-02 gauss-seidel spectral radius is 0.9984267 estimated iterations to convergence 200 setup time was (sec) 1.000000 now iterating at: 12:54:50 rms-change max change #iterations 3.702293 174.1471 at 10iterations 1.622259 55.36269 at 20iterations 0.7162380 26.90739 at 30iterations 0.3169535 11.64384 at 40iterations 0.1401661 4.779922 at 50iterations 6.2017832E-02 1.988312 at 60iterations 2.7586993E-02 0.9095917 at 70iterations 1.2309097E-02 0.4172428 at 80iterations 5.5669262E-03 0.1988611 at 90iterations 2.5694612E-03 9.0217590E-02 at 100iterations 1.2408744E-03 4.6180725E-02 at 110iterations 6.4450433E-04 2.4261475E-02 at 120iterations finished qdiffx linear iterations at : 12:54:59 total time elapsed so far: 9.910000 # loops : 120 mean,max change (kT/e) : 6.4450433E-04 2.4261475E-02 energy calculations done at 9.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.09000 DelPhi exited at 12:54:59 10.093u 0.267s 0:10.88 95.1% 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 12:54:59 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 = 2906 !!! WARNING: CME 304 has a net charge of -0.3480 !!! WARNING: CME 446 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.608993 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): -22.36700 39.03600 ymin,ymax (A): -25.02600 29.29400 zmin,zma (A): -30.21500 27.37000 x,y,z range (A): 61.40300 54.32000 57.58500 scale (grids/A): 2.608993 object centre (A): 8.334499 2.134001 -1.422500 number of atom coordinates read : 2906 total number of charged atoms : 2783 net assigned charge : 0.6990355 assigned positive charge : 426.8130 centred at (gu) : 88.06515 88.11600 97.21678 assigned negative charge : -426.1158 centred at (gu) : 88.16027 88.35128 97.20973 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 170466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29153 grid for indexing accessible points = 1.400000 m= 78486 mr = 118785 m= 25733 mr = 60608 m= 5602 mr = 19101 m= 606 mr = 3738 m= 11 mr = 332 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 4583 time to turn everything in is 1.390000 number of dielectric boundary points 78340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 22253 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) : 1.739329 object centre at (A) : 8.334499 2.134001 -1.422500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1052183 7.7443697E-02 midg,1,midg; midg,igrid,midg 0.2165764 0.1552545 1,midg,midg; igrid,midg,midg 0.1926888 -0.7113125 gauss-seidel spectral radius is 0.9992166 estimated iterations to convergence 282 setup time was (sec) 1.750000 now iterating at: 12:55:01 rms-change max change #iterations 9.394813 321.4337 at 10iterations 5.490739 131.3292 at 20iterations 3.165425 70.09052 at 30iterations 1.823576 40.46862 at 40iterations 1.045532 22.79373 at 50iterations 0.5983152 13.15960 at 60iterations 0.3405746 7.176912 at 70iterations 0.1943211 3.865265 at 80iterations 0.1103975 2.309120 at 90iterations 6.2680811E-02 1.193684 at 100iterations 3.5516154E-02 0.6710186 at 110iterations 2.0132802E-02 0.3762026 at 120iterations 1.1450279E-02 0.2287693 at 130iterations 6.5017510E-03 0.1429596 at 140iterations 3.7108981E-03 8.1560135E-02 at 150iterations 2.1343597E-03 4.1089058E-02 at 160iterations 1.2469564E-03 2.6668549E-02 at 170iterations 7.4452511E-04 1.6958237E-02 at 180iterations finished qdiffx linear iterations at : 12:55:16 total time elapsed so far: 15.97000 # loops : 180 mean,max change (kT/e) : 7.4452511E-04 1.6958237E-02 energy calculations done at 15.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.16000 DelPhi exited at 12:55:16 16.163u 0.309s 0:16.73 98.3% 0+0k 0+0io 0pf+0w