Mon Oct 10 17:07:38 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+sph2.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 = amb2.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 17:07:38 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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: 0.5133974 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): -16.75100 36.16200 ymin,ymax (A): -32.64400 31.29900 zmin,zma (A): -3.826000 65.51600 x,y,z range (A): 52.91300 63.94300 69.34200 scale (grids/A): 0.5133974 object centre (A): 9.705502 -0.6725006 30.84500 number of atom coordinates read : 4291 total number of charged atoms : 4043 net assigned charge : 4.606021 assigned positive charge : 637.6115 centred at (gu) : 90.47830 90.83051 87.52376 assigned negative charge : -633.0092 centred at (gu) : 90.32659 90.87093 87.52147 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7096 nv = 96 ne = 84 npr = 87756 no. pairs analyzed = 87756 no. exposed pairs = 5537 no. arc points = 37758 no. surface atoms = 1847 nbur = 2444 mkacc time = 0.1800000 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= 249 mr = 3624 m= 2 mr = 12 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 0.4100000 number of dielectric boundary points 3711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3624 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2628198E-10 4.2109944E-11 midg,1,midg; midg,igrid,midg 1.4166092E-10 -4.0329476E-11 1,midg,midg; igrid,midg,midg -2.8544686E-10 5.1553184E-10 gauss-seidel spectral radius is 0.9805614 estimated iterations to convergence 59 setup time was (sec) 0.6600000 now iterating at: 17:07:38 rms-change max change #iterations 6.7652769E-02 11.37614 at 10iterations 3.9302940E-03 0.6463432 at 20iterations 4.8685170E-04 7.1498156E-02 at 30iterations 1.7443112E-04 3.1575114E-02 at 40iterations 7.2059702E-05 1.3711333E-02 at 50iterations finished qdiffx linear iterations at : 17:07:41 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 7.2059702E-05 1.3711333E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 17:07:42 3.522u 0.189s 0:04.11 90.0% 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 17:07:42 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.540192 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): -16.75100 36.16200 ymin,ymax (A): -32.64400 31.29900 zmin,zma (A): -3.826000 65.51600 x,y,z range (A): 52.91300 63.94300 69.34200 scale (grids/A): 1.540192 object centre (A): 9.705502 -0.6725006 30.84500 number of atom coordinates read : 4291 total number of charged atoms : 4043 net assigned charge : 4.606021 assigned positive charge : 637.6115 centred at (gu) : 91.43363 92.49060 82.57015 assigned negative charge : -633.0092 centred at (gu) : 90.97955 92.61250 82.56411 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37758 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22647 mr = 54783 m= 1886 mr = 14849 m= 40 mr = 751 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 0.5800000 number of dielectric boundary points 34517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 514 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 30489 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) : 0.5133974 object centre at (A) : 9.705502 -0.6725006 30.84500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8695314E-03 1.1165753E-02 midg,1,midg; midg,igrid,midg -2.0338797E-03 -8.1633357E-03 1,midg,midg; igrid,midg,midg -3.5856203E-03 1.1884753E-02 gauss-seidel spectral radius is 0.9980852 estimated iterations to convergence 182 setup time was (sec) 0.8700000 now iterating at: 17:07:43 rms-change max change #iterations 3.592470 152.0080 at 10iterations 1.456691 50.61202 at 20iterations 0.5929314 20.49611 at 30iterations 0.2411888 9.446074 at 40iterations 9.8076120E-02 3.355179 at 50iterations 4.0112402E-02 1.335527 at 60iterations 1.6313650E-02 0.5456114 at 70iterations 6.7174505E-03 0.2247734 at 80iterations 2.7702914E-03 8.7471008E-02 at 90iterations 1.1720642E-03 4.0954590E-02 at 100iterations 5.2140467E-04 1.8035889E-02 at 110iterations 2.5905788E-04 8.8539124E-03 at 120iterations finished qdiffx linear iterations at : 17:07:50 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.5905788E-04 8.8539124E-03 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 17:07:50 7.769u 0.259s 0:08.49 94.3% 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 17:07:50 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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: 2.310288 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): -16.75100 36.16200 ymin,ymax (A): -32.64400 31.29900 zmin,zma (A): -3.826000 65.51600 x,y,z range (A): 52.91300 63.94300 69.34200 scale (grids/A): 2.310288 object centre (A): 9.705502 -0.6725006 30.84500 number of atom coordinates read : 4291 total number of charged atoms : 4043 net assigned charge : 4.606021 assigned positive charge : 637.6115 centred at (gu) : 92.15028 93.73538 78.85500 assigned negative charge : -633.0092 centred at (gu) : 91.46933 93.91863 78.84596 start vw surface at 0.2000000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 187084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37758 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81643 mr = 134303 m= 20016 mr = 63420 m= 2572 mr = 14184 m= 130 mr = 1521 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 1882 time to turn everything in is 1.390000 number of dielectric boundary points 77982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 32253 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) : 1.540192 object centre at (A) : 9.705502 -0.6725006 30.84500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1228287 0.3001784 midg,1,midg; midg,igrid,midg -9.7792499E-02 -0.1950515 1,midg,midg; igrid,midg,midg -5.0519403E-02 0.1786707 gauss-seidel spectral radius is 0.9991423 estimated iterations to convergence 270 setup time was (sec) 1.690000 now iterating at: 17:07:52 rms-change max change #iterations 9.709730 285.2485 at 10iterations 5.530192 137.0151 at 20iterations 3.123467 75.49203 at 30iterations 1.756190 43.78493 at 40iterations 0.9848093 23.47579 at 50iterations 0.5491883 12.09660 at 60iterations 0.3060080 6.716750 at 70iterations 0.1697310 4.292005 at 80iterations 9.4355881E-02 2.295662 at 90iterations 5.2251454E-02 1.124905 at 100iterations 2.8901568E-02 0.6357555 at 110iterations 1.6009478E-02 0.3418579 at 120iterations 8.8555245E-03 0.1934252 at 130iterations 4.9016061E-03 0.1107903 at 140iterations 2.7092563E-03 5.3810120E-02 at 150iterations 1.5053768E-03 3.1391144E-02 at 160iterations 8.4086653E-04 1.7467618E-02 at 170iterations 4.7462093E-04 1.0802507E-02 at 180iterations finished qdiffx linear iterations at : 17:08:03 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 4.7462093E-04 1.0802507E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 17:08:04 12.580u 0.245s 0:13.18 97.2% 0+0k 0+0io 0pf+0w