Tue Oct 11 03:14:36 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 Tue Oct 11 2011 at 03:14:37 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 = 2112 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: 0.6969050 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): -34.60000 11.64400 ymin,ymax (A): -16.34500 28.04400 zmin,zma (A): -26.51900 24.56400 x,y,z range (A): 46.24400 44.38900 51.08300 scale (grids/A): 0.6969050 object centre (A): -11.47800 5.849501 -0.9775009 number of atom coordinates read : 2112 total number of charged atoms : 2002 net assigned charge : 3.000008 assigned positive charge : 314.3515 centred at (gu) : 89.52280 90.81798 89.21501 assigned negative charge : -311.3520 centred at (gu) : 89.51900 90.81487 89.00488 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7080 nv = 96 ne = 84 npr = 43199 no. pairs analyzed = 43199 no. exposed pairs = 2703 no. arc points = 18797 no. surface atoms = 909 nbur = 1203 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 3943 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1698 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3994599E-08 8.5792202E-08 midg,1,midg; midg,igrid,midg 1.6475997E-08 2.5348170E-08 1,midg,midg; igrid,midg,midg 2.0776200E-08 2.0007301E-08 gauss-seidel spectral radius is 0.9892808 estimated iterations to convergence 79 setup time was (sec) 0.5900000 now iterating at: 03:14:38 rms-change max change #iterations 0.1926921 25.59177 at 10iterations 2.2823868E-02 3.349283 at 20iterations 2.7902420E-03 0.3850670 at 30iterations 3.7023940E-04 5.0189972E-02 at 40iterations 6.7684814E-05 1.1544228E-02 at 50iterations finished qdiffx linear iterations at : 03:14:42 total time elapsed so far: 4.920000 # loops : 50 mean,max change (kT/e) : 6.7684814E-05 1.1544228E-02 energy calculations done at 4.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.090000 DelPhi exited at 03:14:42 5.091u 0.420s 0:05.90 93.3% 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 Tue Oct 11 2011 at 03:14:43 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 = 2112 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: 2.090715 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): -34.60000 11.64400 ymin,ymax (A): -16.34500 28.04400 zmin,zma (A): -26.51900 24.56400 x,y,z range (A): 46.24400 44.38900 51.08300 scale (grids/A): 2.090715 object centre (A): -11.47800 5.849501 -0.9775009 number of atom coordinates read : 2112 total number of charged atoms : 2002 net assigned charge : 3.000008 assigned positive charge : 314.3515 centred at (gu) : 88.56823 92.45353 87.64462 assigned negative charge : -311.3520 centred at (gu) : 88.55689 92.44460 87.01476 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 75167 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18797 grid for indexing accessible points = 1.400000 m= 28016 mr = 52320 m= 5376 mr = 20760 m= 473 mr = 3437 m= 10 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 32328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15890 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) : 0.6969050 object centre at (A) : -11.47800 5.849501 -0.9775009 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0901377E-02 7.2154604E-02 midg,1,midg; midg,igrid,midg 1.1444565E-02 -8.0147590E-03 1,midg,midg; igrid,midg,midg -3.6538273E-02 9.9458480E-03 gauss-seidel spectral radius is 0.9988117 estimated iterations to convergence 230 setup time was (sec) 0.9500000 now iterating at: 03:14:44 rms-change max change #iterations 4.527127 193.1506 at 10iterations 2.219659 74.46088 at 20iterations 1.104212 33.07112 at 30iterations 0.5429077 16.33406 at 40iterations 0.2679949 10.11752 at 50iterations 0.1324527 4.126694 at 60iterations 6.5192252E-02 1.854362 at 70iterations 3.2262284E-02 1.030852 at 80iterations 1.5909508E-02 0.4651489 at 90iterations 7.8695854E-03 0.2234547 at 100iterations 3.8800142E-03 0.1199036 at 110iterations 1.9199986E-03 5.8586121E-02 at 120iterations finished qdiffx linear iterations at : 03:14:56 total time elapsed so far: 12.50000 # loops : 120 mean,max change (kT/e) : 1.9199986E-03 5.8586121E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 03:14:56 12.656u 0.537s 0:13.53 97.4% 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 Tue Oct 11 2011 at 03:14:56 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 = 2112 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: 3.136073 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): -34.60000 11.64400 ymin,ymax (A): -16.34500 28.04400 zmin,zma (A): -26.51900 24.56400 x,y,z range (A): 46.24400 44.38900 51.08300 scale (grids/A): 3.136073 object centre (A): -11.47800 5.849501 -0.9775009 number of atom coordinates read : 2112 total number of charged atoms : 2002 net assigned charge : 3.000008 assigned positive charge : 314.3515 centred at (gu) : 87.85221 93.68024 86.46690 assigned negative charge : -311.3520 centred at (gu) : 87.83542 93.66699 85.52209 start vw surface at 0.1000000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 174054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18797 grid for indexing accessible points = 1.400000 m= 88449 mr = 126931 m= 34881 mr = 72579 m= 9952 mr = 28061 m= 1873 mr = 7581 m= 186 mr = 1264 m= 12 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.970000 number of dielectric boundary points 72895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 16016 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) : 2.090715 object centre at (A) : -11.47800 5.849501 -0.9775009 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7524720 0.5808642 midg,1,midg; midg,igrid,midg 8.8399284E-02 -0.1122623 1,midg,midg; igrid,midg,midg -0.3668444 0.1162351 gauss-seidel spectral radius is 0.9993042 estimated iterations to convergence 299 setup time was (sec) 2.340000 now iterating at: 03:14:59 rms-change max change #iterations 10.17235 402.5826 at 10iterations 5.995020 143.1324 at 20iterations 3.539607 78.30820 at 30iterations 2.080830 54.16262 at 40iterations 1.221794 22.70941 at 50iterations 0.7169468 12.48849 at 60iterations 0.4211401 8.684483 at 70iterations 0.2463378 4.333227 at 80iterations 0.1439519 2.513658 at 90iterations 8.4477849E-02 1.468130 at 100iterations 4.9436860E-02 0.8448105 at 110iterations 2.8831104E-02 0.4696975 at 120iterations 1.6889049E-02 0.2869673 at 130iterations 9.8535344E-03 0.1678729 at 140iterations 5.7770549E-03 0.1023903 at 150iterations 3.3729195E-03 5.6581497E-02 at 160iterations 1.9760337E-03 3.5689354E-02 at 170iterations 1.1639319E-03 1.9337654E-02 at 180iterations finished qdiffx linear iterations at : 03:15:17 total time elapsed so far: 20.53000 # loops : 180 mean,max change (kT/e) : 1.1639319E-03 1.9337654E-02 energy calculations done at 20.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.69000 DelPhi exited at 03:15:18 20.699u 0.539s 0:21.79 97.3% 0+0k 0+0io 0pf+0w