Sat Oct 8 11:38:27 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+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 8 2011 at 11:38:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 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: 0.5770789 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): -4.606000 39.08700 ymin,ymax (A): 21.70700 83.39700 zmin,zma (A): 26.43200 81.79601 x,y,z range (A): 43.69300 61.69000 55.36401 scale (grids/A): 0.5770789 object centre (A): 17.24050 52.55200 54.11400 number of atom coordinates read : 2619 total number of charged atoms : 2469 net assigned charge : 1.000007 assigned positive charge : 385.2937 centred at (gu) : 90.68144 90.40977 89.86613 assigned negative charge : -384.2944 centred at (gu) : 90.62228 90.27155 89.91834 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5660 nv = 96 ne = 84 npr = 52843 no. pairs analyzed = 52843 no. exposed pairs = 3371 no. arc points = 23418 no. surface atoms = 1145 nbur = 1474 mkacc time = 0.1400000 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= 284 mr = 2925 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2313 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 7188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1103914E-09 -7.0483785E-10 midg,1,midg; midg,igrid,midg -2.0374338E-09 2.7881470E-09 1,midg,midg; igrid,midg,midg -7.2097628E-10 1.4050533E-09 gauss-seidel spectral radius is 0.9844746 estimated iterations to convergence 66 setup time was (sec) 0.8600000 now iterating at: 11:38:29 rms-change max change #iterations 8.8723592E-02 19.43905 at 10iterations 6.8718544E-03 1.147366 at 20iterations 5.5018131E-04 7.8769684E-02 at 30iterations 6.5494605E-05 1.3121128E-02 at 40iterations 1.8422208E-05 4.4164658E-03 at 50iterations finished qdiffx linear iterations at : 11:38:36 total time elapsed so far: 7.690000 # loops : 50 mean,max change (kT/e) : 1.8422208E-05 4.4164658E-03 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 11:38:36 7.874u 0.635s 0:09.03 94.1% 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 8 2011 at 11:38:36 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 = 2619 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: 1.731237 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): -4.606000 39.08700 ymin,ymax (A): 21.70700 83.39700 zmin,zma (A): 26.43200 81.79601 x,y,z range (A): 43.69300 61.69000 55.36401 scale (grids/A): 1.731237 object centre (A): 17.24050 52.55200 54.11400 number of atom coordinates read : 2619 total number of charged atoms : 2469 net assigned charge : 1.000007 assigned positive charge : 385.2937 centred at (gu) : 92.04376 91.22865 89.59747 assigned negative charge : -384.2944 centred at (gu) : 91.86642 90.81435 89.75490 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23418 grid for indexing accessible points = 1.400000 m= 19136 mr = 41631 m= 2418 mr = 13192 m= 88 mr = 1314 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 27704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19152 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) : 0.5770789 object centre at (A) : 17.24050 52.55200 54.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0999007E-04 -1.6164236E-02 midg,1,midg; midg,igrid,midg 9.4229355E-03 2.0962112E-02 1,midg,midg; igrid,midg,midg -7.8166334E-04 5.1408149E-03 gauss-seidel spectral radius is 0.9983534 estimated iterations to convergence 196 setup time was (sec) 1.000000 now iterating at: 11:38:38 rms-change max change #iterations 3.468455 163.1814 at 10iterations 1.499496 74.66762 at 20iterations 0.6473187 27.73671 at 30iterations 0.2813862 10.49406 at 40iterations 0.1222391 4.284280 at 50iterations 5.3144772E-02 1.978768 at 60iterations 2.3201715E-02 0.7760448 at 70iterations 1.0069608E-02 0.3598595 at 80iterations 4.3930877E-03 0.1682024 at 90iterations 1.9273091E-03 6.1831713E-02 at 100iterations 8.6161256E-04 4.2857170E-02 at 110iterations 4.0220219E-04 1.5642166E-02 at 120iterations finished qdiffx linear iterations at : 11:38:56 total time elapsed so far: 19.63000 # loops : 120 mean,max change (kT/e) : 4.0220219E-04 1.5642166E-02 energy calculations done at 19.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.81000 DelPhi exited at 11:38:57 19.814u 0.629s 0:20.71 98.6% 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 8 2011 at 11:38:57 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 = 2619 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: 2.596855 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): -4.606000 39.08700 ymin,ymax (A): 21.70700 83.39700 zmin,zma (A): 26.43200 81.79601 x,y,z range (A): 43.69300 61.69000 55.36401 scale (grids/A): 2.596855 object centre (A): 17.24050 52.55200 54.11400 number of atom coordinates read : 2619 total number of charged atoms : 2469 net assigned charge : 1.000007 assigned positive charge : 385.2937 centred at (gu) : 93.06533 91.84282 89.39615 assigned negative charge : -384.2944 centred at (gu) : 92.79959 91.22151 89.63227 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 144199 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23418 grid for indexing accessible points = 1.400000 m= 65383 mr = 101746 m= 19917 mr = 51606 m= 4003 mr = 15100 m= 388 mr = 2775 m= 11 mr = 198 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 62476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 19747 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) : 1.731237 object centre at (A) : 17.24050 52.55200 54.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2228652E-03 -0.1988461 midg,1,midg; midg,igrid,midg 0.2393914 0.2849864 1,midg,midg; igrid,midg,midg -2.9687237E-03 4.9737781E-02 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 2.160000 now iterating at: 11:39:00 rms-change max change #iterations 8.584111 278.6556 at 10iterations 4.869344 121.8463 at 20iterations 2.752741 63.48248 at 30iterations 1.549741 38.85009 at 40iterations 0.8698733 22.64436 at 50iterations 0.4886498 11.35872 at 60iterations 0.2732134 6.336373 at 70iterations 0.1532892 3.275364 at 80iterations 8.5647993E-02 1.943260 at 90iterations 4.7843181E-02 0.9878645 at 100iterations 2.6779227E-02 0.5820904 at 110iterations 1.4954486E-02 0.3926888 at 120iterations 8.3726784E-03 0.1781560 at 130iterations 4.7041681E-03 0.1103072 at 140iterations 2.6604317E-03 6.0405731E-02 at 150iterations 1.5304228E-03 3.6978722E-02 at 160iterations 9.0585736E-04 2.6060581E-02 at 170iterations 5.6446216E-04 1.4223099E-02 at 180iterations finished qdiffx linear iterations at : 11:39:28 total time elapsed so far: 29.62000 # loops : 180 mean,max change (kT/e) : 5.6446216E-04 1.4223099E-02 energy calculations done at 29.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.78000 DelPhi exited at 11:39:28 29.789u 0.863s 0:31.00 98.8% 0+0k 0+0io 0pf+0w