Sun Oct 9 09:56:39 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 Sun Oct 9 2011 at 09:56:39 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 = 2837 !!! WARNING: ASP 494 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6029096 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): -14.01700 40.03200 ymin,ymax (A): -25.48600 33.56100 zmin,zma (A): -2.162000 48.78500 x,y,z range (A): 54.04900 59.04700 50.94700 scale (grids/A): 0.6029096 object centre (A): 13.00750 4.037500 23.31150 number of atom coordinates read : 2837 total number of charged atoms : 2721 net assigned charge : 1.000016 assigned positive charge : 417.1552 centred at (gu) : 89.88432 89.89888 90.70234 assigned negative charge : -416.1568 centred at (gu) : 89.76759 89.97048 90.67785 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7042 nv = 96 ne = 84 npr = 56187 no. pairs analyzed = 56187 no. exposed pairs = 3868 no. arc points = 26823 no. surface atoms = 1286 nbur = 1551 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3602 m= 3 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2729 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9204518E-10 1.7774483E-09 midg,1,midg; midg,igrid,midg 3.5917174E-09 -2.5604476E-09 1,midg,midg; igrid,midg,midg -4.7204978E-09 5.2588862E-09 gauss-seidel spectral radius is 0.9857925 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 09:56:40 rms-change max change #iterations 0.1124780 18.22432 at 10iterations 9.6589811E-03 1.439655 at 20iterations 8.9273066E-04 0.1333275 at 30iterations 1.0523378E-04 1.5213013E-02 at 40iterations 1.8575483E-05 3.2310486E-03 at 50iterations finished qdiffx linear iterations at : 09:56:43 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.8575483E-05 3.2310486E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 09:56:43 3.440u 0.177s 0:03.90 92.5% 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 Sun Oct 9 2011 at 09:56:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 !!! WARNING: ASP 494 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.808729 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): -14.01700 40.03200 ymin,ymax (A): -25.48600 33.56100 zmin,zma (A): -2.162000 48.78500 x,y,z range (A): 54.04900 59.04700 50.94700 scale (grids/A): 1.808729 object centre (A): 13.00750 4.037500 23.31150 number of atom coordinates read : 2837 total number of charged atoms : 2721 net assigned charge : 1.000016 assigned positive charge : 417.1552 centred at (gu) : 89.65231 89.69564 92.10616 assigned negative charge : -416.1568 centred at (gu) : 89.30264 89.91129 92.03370 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26823 grid for indexing accessible points = 1.400000 m= 26902 mr = 51522 m= 4220 mr = 18644 m= 227 mr = 2414 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.3900000 number of dielectric boundary points 35160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 21310 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) : 0.6029096 object centre at (A) : 13.00750 4.037500 23.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9438213E-03 3.5163173E-03 midg,1,midg; midg,igrid,midg -1.1048457E-02 -2.9220186E-02 1,midg,midg; igrid,midg,midg -8.4651047E-03 2.1337172E-02 gauss-seidel spectral radius is 0.9985371 estimated iterations to convergence 207 setup time was (sec) 0.6000000 now iterating at: 09:56:44 rms-change max change #iterations 3.967158 171.6973 at 10iterations 1.805436 64.07278 at 20iterations 0.8220555 27.51383 at 30iterations 0.3746166 12.64905 at 40iterations 0.1708023 5.642326 at 50iterations 7.7471025E-02 2.481286 at 60iterations 3.5386484E-02 1.193658 at 70iterations 1.6176047E-02 0.5365162 at 80iterations 7.3864381E-03 0.2609138 at 90iterations 3.3763393E-03 0.1229401 at 100iterations 1.5483222E-03 5.2024841E-02 at 110iterations 7.1068626E-04 2.1390438E-02 at 120iterations finished qdiffx linear iterations at : 09:56:51 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 7.1068626E-04 2.1390438E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 09:56:52 7.906u 0.208s 0:08.38 96.6% 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 Sun Oct 9 2011 at 09:56:52 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 = 2837 !!! WARNING: ASP 494 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.713093 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): -14.01700 40.03200 ymin,ymax (A): -25.48600 33.56100 zmin,zma (A): -2.162000 48.78500 x,y,z range (A): 54.04900 59.04700 50.94700 scale (grids/A): 2.713093 object centre (A): 13.00750 4.037500 23.31150 number of atom coordinates read : 2837 total number of charged atoms : 2721 net assigned charge : 1.000016 assigned positive charge : 417.1552 centred at (gu) : 89.47821 89.54328 93.15894 assigned negative charge : -416.1568 centred at (gu) : 88.95396 89.86687 93.05051 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 176973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26823 grid for indexing accessible points = 1.400000 m= 86923 mr = 125987 m= 31005 mr = 68475 m= 7463 mr = 23698 m= 950 mr = 5235 m= 34 mr = 561 m= 0 mr = 2 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1159 time to turn everything in is 0.9600000 number of dielectric boundary points 79390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 21763 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) : 1.808729 object centre at (A) : 13.00750 4.037500 23.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3933509E-02 2.3064207E-02 midg,1,midg; midg,igrid,midg -0.1241011 -0.9901244 1,midg,midg; igrid,midg,midg -7.9024322E-02 0.2917937 gauss-seidel spectral radius is 0.9992504 estimated iterations to convergence 288 setup time was (sec) 1.190000 now iterating at: 09:56:53 rms-change max change #iterations 9.855147 333.3056 at 10iterations 5.864333 179.5571 at 20iterations 3.443427 91.17758 at 30iterations 2.012971 44.32915 at 40iterations 1.170210 26.50261 at 50iterations 0.6795482 16.09178 at 60iterations 0.3922286 8.624821 at 70iterations 0.2262409 4.478662 at 80iterations 0.1302921 2.785786 at 90iterations 7.5028971E-02 1.626028 at 100iterations 4.3145794E-02 0.8882809 at 110iterations 2.4763163E-02 0.4761887 at 120iterations 1.4234120E-02 0.2654238 at 130iterations 8.1660794E-03 0.1547623 at 140iterations 4.6914034E-03 9.0674192E-02 at 150iterations 2.6872256E-03 5.8876038E-02 at 160iterations 1.5474998E-03 2.6936531E-02 at 170iterations 8.9117099E-04 1.6496658E-02 at 180iterations finished qdiffx linear iterations at : 09:57:04 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 8.9117099E-04 1.6496658E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 09:57:05 12.617u 0.216s 0:13.09 97.9% 0+0k 0+0io 0pf+0w