Mon Oct 10 17:02:38 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 Mon Oct 10 2011 at 17:02:38 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4783 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5129979 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): -17.37400 36.71700 ymin,ymax (A): -30.95500 33.93100 zmin,zma (A): -3.866000 65.53000 x,y,z range (A): 54.09100 64.88600 69.39600 scale (grids/A): 0.5129979 object centre (A): 9.671501 1.488000 30.83200 number of atom coordinates read : 4783 total number of charged atoms : 4537 net assigned charge : 6.800027 assigned positive charge : 717.5475 centred at (gu) : 90.07798 90.62090 88.36719 assigned negative charge : -710.7518 centred at (gu) : 89.96764 90.65813 88.33598 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8014 nv = 96 ne = 84 npr = 96583 no. pairs analyzed = 96583 no. exposed pairs = 6189 no. arc points = 42714 no. surface atoms = 2058 nbur = 2725 mkacc time = 0.2600000 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 = 1.652000 m= 297 mr = 4101 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4105 ## 583 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10574 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7814143E-11 1.2985972E-10 midg,1,midg; midg,igrid,midg 1.8278548E-10 2.2437711E-12 1,midg,midg; igrid,midg,midg -2.0532441E-10 4.2769346E-10 gauss-seidel spectral radius is 0.9805699 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 17:02:39 rms-change max change #iterations 6.9570109E-02 9.607681 at 10iterations 4.1107396E-03 0.6261482 at 20iterations 4.8743832E-04 6.8905354E-02 at 30iterations 1.7064399E-04 2.8375864E-02 at 40iterations 6.8703732E-05 1.1669159E-02 at 50iterations finished qdiffx linear iterations at : 17:02:41 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 6.8703732E-05 1.1669159E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 17:02:42 3.548u 0.147s 0:04.39 83.8% 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 Mon Oct 10 2011 at 17:02:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4783 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.538994 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): -17.37400 36.71700 ymin,ymax (A): -30.95500 33.93100 zmin,zma (A): -3.866000 65.53000 x,y,z range (A): 54.09100 64.88600 69.39600 scale (grids/A): 1.538994 object centre (A): 9.671501 1.488000 30.83200 number of atom coordinates read : 4783 total number of charged atoms : 4537 net assigned charge : 6.800027 assigned positive charge : 717.5475 centred at (gu) : 90.23280 91.86159 85.09999 assigned negative charge : -710.7518 centred at (gu) : 89.90251 91.97406 85.00755 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 90742 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42714 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25661 mr = 62053 m= 2219 mr = 16689 m= 51 mr = 919 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 229 time to turn everything in is 0.6800000 number of dielectric boundary points 39010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 577 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 34228 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) : 0.5129979 object centre at (A) : 9.671501 1.488000 30.83200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7056983E-03 2.1872018E-02 midg,1,midg; midg,igrid,midg 5.3363014E-04 -1.1291190E-02 1,midg,midg; igrid,midg,midg -1.5171139E-03 1.0449995E-02 gauss-seidel spectral radius is 0.9981374 estimated iterations to convergence 184 setup time was (sec) 0.9700000 now iterating at: 17:02:43 rms-change max change #iterations 3.856967 163.6129 at 10iterations 1.585710 53.73414 at 20iterations 0.6538210 20.00797 at 30iterations 0.2698878 9.834909 at 40iterations 0.1113902 3.803034 at 50iterations 4.6167031E-02 1.563061 at 60iterations 1.9067373E-02 0.5638428 at 70iterations 7.8836139E-03 0.2591248 at 80iterations 3.2967199E-03 0.1012065 at 90iterations 1.4017901E-03 4.6060562E-02 at 100iterations 6.2318111E-04 1.9641399E-02 at 110iterations 3.0508800E-04 1.1027217E-02 at 120iterations finished qdiffx linear iterations at : 17:02:50 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 3.0508800E-04 1.1027217E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 17:02:52 7.645u 0.183s 0:09.33 83.8% 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 Mon Oct 10 2011 at 17:02:52 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4783 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.308491 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): -17.37400 36.71700 ymin,ymax (A): -30.95500 33.93100 zmin,zma (A): -3.866000 65.53000 x,y,z range (A): 54.09100 64.88600 69.39600 scale (grids/A): 2.308491 object centre (A): 9.671501 1.488000 30.83200 number of atom coordinates read : 4783 total number of charged atoms : 4537 net assigned charge : 6.800027 assigned positive charge : 717.5475 centred at (gu) : 90.34871 92.79205 82.64976 assigned negative charge : -710.7518 centred at (gu) : 89.85376 92.96098 82.51134 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 211778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42714 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92797 mr = 152833 m= 22572 mr = 71812 m= 3091 mr = 15749 m= 165 mr = 1799 m= 0 mr = 67 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 760 time to turn everything in is 1.570000 number of dielectric boundary points 88143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 36223 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) : 1.538994 object centre at (A) : 9.671501 1.488000 30.83200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1324133 0.5005195 midg,1,midg; midg,igrid,midg -0.1055952 -0.2779778 1,midg,midg; igrid,midg,midg -2.1498367E-02 0.1491492 gauss-seidel spectral radius is 0.9991723 estimated iterations to convergence 274 setup time was (sec) 1.880000 now iterating at: 17:02:54 rms-change max change #iterations 10.39191 271.1002 at 10iterations 5.985069 141.9144 at 20iterations 3.427043 104.2711 at 30iterations 1.939650 44.05323 at 40iterations 1.098926 28.81012 at 50iterations 0.6198673 15.32733 at 60iterations 0.3491812 7.361465 at 70iterations 0.1958740 3.671506 at 80iterations 0.1097354 2.401062 at 90iterations 6.1398584E-02 1.209843 at 100iterations 3.4346372E-02 0.7686253 at 110iterations 1.9234596E-02 0.3728218 at 120iterations 1.0764427E-02 0.2214890 at 130iterations 6.0049267E-03 0.1151118 at 140iterations 3.3679549E-03 7.0724487E-02 at 150iterations 1.8924677E-03 3.5062790E-02 at 160iterations 1.0711746E-03 2.3358345E-02 at 170iterations 6.1468233E-04 1.2399673E-02 at 180iterations finished qdiffx linear iterations at : 17:03:06 total time elapsed so far: 13.86000 # loops : 180 mean,max change (kT/e) : 6.1468233E-04 1.2399673E-02 energy calculations done at 13.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.06000 DelPhi exited at 17:03:07 14.065u 0.181s 0:14.93 95.3% 0+0k 0+0io 0pf+0w