Sat Oct 8 12:48:10 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 12:48:10 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 = 2344 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: 0.6054834 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): 30.17600 88.97200 ymin,ymax (A): -5.350000 37.42900 zmin,zma (A): -13.52100 44.46800 x,y,z range (A): 58.79600 42.77900 57.98900 scale (grids/A): 0.6054834 object centre (A): 59.57400 16.03950 15.47350 number of atom coordinates read : 2344 total number of charged atoms : 2209 net assigned charge : -1.999999 assigned positive charge : 318.2606 centred at (gu) : 89.43571 89.19878 87.90946 assigned negative charge : -320.2611 centred at (gu) : 89.62070 89.14871 87.95754 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5787 nv = 96 ne = 84 npr = 49921 no. pairs analyzed = 49921 no. exposed pairs = 3045 no. arc points = 21373 no. surface atoms = 1041 nbur = 1303 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 = 1.456000 m= 257 mr = 2884 m= 0 mr = 7 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2003 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0480303E-09 -1.7517092E-09 midg,1,midg; midg,igrid,midg -3.4273859E-09 5.6594185E-10 1,midg,midg; igrid,midg,midg 6.0904282E-09 -6.8352217E-09 gauss-seidel spectral radius is 0.9858689 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 12:48:11 rms-change max change #iterations 0.1026618 17.30660 at 10iterations 8.7492485E-03 1.452705 at 20iterations 8.1372296E-04 0.1275253 at 30iterations 8.3740910E-05 1.4339447E-02 at 40iterations 1.0613539E-05 1.8386841E-03 at 50iterations finished qdiffx linear iterations at : 12:48:15 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.0613539E-05 1.8386841E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 12:48:15 4.181u 0.284s 0:04.75 93.8% 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 Sat Oct 8 2011 at 12:48:15 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 = 2344 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: 1.816450 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): 30.17600 88.97200 ymin,ymax (A): -5.350000 37.42900 zmin,zma (A): -13.52100 44.46800 x,y,z range (A): 58.79600 42.77900 57.98900 scale (grids/A): 1.816450 object centre (A): 59.57400 16.03950 15.47350 number of atom coordinates read : 2344 total number of charged atoms : 2209 net assigned charge : -1.999999 assigned positive charge : 318.2606 centred at (gu) : 88.30689 87.59605 83.72795 assigned negative charge : -320.2611 centred at (gu) : 88.86204 87.44627 83.87282 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21373 grid for indexing accessible points = 1.400000 m= 19778 mr = 41474 m= 2628 mr = 13249 m= 81 mr = 1412 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 73 time to turn everything in is 0.5600000 number of dielectric boundary points 29298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17297 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) : 0.6054834 object centre at (A) : 59.57400 16.03950 15.47350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1301923E-02 7.2607021E-03 midg,1,midg; midg,igrid,midg -8.2221106E-03 -1.4253159E-03 1,midg,midg; igrid,midg,midg 2.1130145E-02 -2.9837865E-02 gauss-seidel spectral radius is 0.9984788 estimated iterations to convergence 203 setup time was (sec) 0.8800000 now iterating at: 12:48:16 rms-change max change #iterations 3.444406 180.7094 at 10iterations 1.536561 61.99394 at 20iterations 0.6917090 26.82930 at 30iterations 0.3102171 11.44016 at 40iterations 0.1392307 4.995695 at 50iterations 6.2666312E-02 2.283569 at 60iterations 2.8083602E-02 1.004826 at 70iterations 1.2609542E-02 0.4407883 at 80iterations 5.6600841E-03 0.1868997 at 90iterations 2.5488937E-03 8.3123207E-02 at 100iterations 1.1531080E-03 3.8717270E-02 at 110iterations 5.2260980E-04 2.0314544E-02 at 120iterations finished qdiffx linear iterations at : 12:48:25 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 5.2260980E-04 2.0314544E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 12:48:25 9.596u 0.335s 0:10.20 97.2% 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 Sat Oct 8 2011 at 12:48:25 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 = 2344 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: 2.724675 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): 30.17600 88.97200 ymin,ymax (A): -5.350000 37.42900 zmin,zma (A): -13.52100 44.46800 x,y,z range (A): 58.79600 42.77900 57.98900 scale (grids/A): 2.724675 object centre (A): 59.57400 16.03950 15.47350 number of atom coordinates read : 2344 total number of charged atoms : 2209 net assigned charge : -1.999999 assigned positive charge : 318.2606 centred at (gu) : 87.46021 86.39409 80.59181 assigned negative charge : -320.2611 centred at (gu) : 88.29308 86.16943 80.80927 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 146092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21373 grid for indexing accessible points = 1.400000 m= 65859 mr = 101529 m= 21145 mr = 51252 m= 4391 mr = 15859 m= 387 mr = 3010 m= 14 mr = 200 m= 0 mr = 4 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 1.430000 number of dielectric boundary points 66034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 17670 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) : 1.816450 object centre at (A) : 59.57400 16.03950 15.47350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9656129E-02 8.6343370E-02 midg,1,midg; midg,igrid,midg -7.2929934E-02 -4.2974004E-03 1,midg,midg; igrid,midg,midg 0.3690073 -0.3458215 gauss-seidel spectral radius is 0.9992129 estimated iterations to convergence 281 setup time was (sec) 1.750000 now iterating at: 12:48:27 rms-change max change #iterations 8.277021 264.1747 at 10iterations 4.762150 174.0056 at 20iterations 2.715175 63.47578 at 30iterations 1.540206 41.32919 at 40iterations 0.8722978 21.28454 at 50iterations 0.4950975 11.11547 at 60iterations 0.2805124 5.747556 at 70iterations 0.1581309 3.412231 at 80iterations 8.9567393E-02 1.785116 at 90iterations 5.0506976E-02 0.9980431 at 100iterations 2.8488725E-02 0.5347366 at 110iterations 1.6075719E-02 0.3199844 at 120iterations 9.0991473E-03 0.1764097 at 130iterations 5.1336573E-03 9.8934412E-02 at 140iterations 2.9011131E-03 5.7956696E-02 at 150iterations 1.6408887E-03 3.3002853E-02 at 160iterations 9.2980271E-04 1.8981934E-02 at 170iterations 5.3029350E-04 1.0811090E-02 at 180iterations finished qdiffx linear iterations at : 12:48:41 total time elapsed so far: 15.63000 # loops : 180 mean,max change (kT/e) : 5.3029350E-04 1.0811090E-02 energy calculations done at 15.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.81000 DelPhi exited at 12:48:42 15.814u 0.325s 0:16.39 98.4% 0+0k 0+0io 0pf+0w