Mon Oct 10 14:03:13 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 14:03:13 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2121 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7477578 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): -21.06800 24.68400 ymin,ymax (A): -8.027000 36.62000 zmin,zma (A): -3.577000 44.03200 x,y,z range (A): 45.75200 44.64700 47.60900 scale (grids/A): 0.7477578 object centre (A): 1.808000 14.29650 20.22750 number of atom coordinates read : 2121 total number of charged atoms : 1981 net assigned charge : -4.771990 assigned positive charge : 317.4509 centred at (gu) : 88.95057 90.37772 90.43271 assigned negative charge : -322.2230 centred at (gu) : 88.93632 90.41768 90.56082 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8126 nv = 96 ne = 84 npr = 43731 no. pairs analyzed = 43731 no. exposed pairs = 2721 no. arc points = 19063 no. surface atoms = 922 nbur = 1199 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 584 mr = 4516 m= 4 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1512 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8591509E-08 -2.7413503E-07 midg,1,midg; midg,igrid,midg -4.7333288E-08 -1.5630090E-07 1,midg,midg; igrid,midg,midg -1.3909802E-07 -6.7405104E-08 gauss-seidel spectral radius is 0.9906797 estimated iterations to convergence 84 setup time was (sec) 0.4900000 now iterating at: 14:03:14 rms-change max change #iterations 0.2625723 36.91623 at 10iterations 3.5721753E-02 5.172016 at 20iterations 4.9320194E-03 0.5928392 at 30iterations 6.7855918E-04 9.0080261E-02 at 40iterations 9.4271847E-05 1.3201714E-02 at 50iterations finished qdiffx linear iterations at : 14:03:16 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 9.4271847E-05 1.3201714E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 14:03:17 3.290u 0.201s 0:04.14 84.2% 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 Mon Oct 10 2011 at 14:03:17 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2121 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.243273 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): -21.06800 24.68400 ymin,ymax (A): -8.027000 36.62000 zmin,zma (A): -3.577000 44.03200 x,y,z range (A): 45.75200 44.64700 47.60900 scale (grids/A): 2.243273 object centre (A): 1.808000 14.29650 20.22750 number of atom coordinates read : 2121 total number of charged atoms : 1981 net assigned charge : -4.771990 assigned positive charge : 317.4509 centred at (gu) : 86.85155 91.13316 91.29800 assigned negative charge : -322.2230 centred at (gu) : 86.80904 91.25296 91.68261 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 85400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19063 grid for indexing accessible points = 1.400000 m= 33907 mr = 58921 m= 7351 mr = 25626 m= 808 mr = 5050 m= 24 mr = 433 m= 0 mr = 4 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 37456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15780 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) : 0.7477578 object centre at (A) : 1.808000 14.29650 20.22750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1873441E-03 -0.1160247 midg,1,midg; midg,igrid,midg -2.8875962E-02 -3.5341427E-02 1,midg,midg; igrid,midg,midg 1.4531468E-03 -6.5629982E-04 gauss-seidel spectral radius is 0.9989456 estimated iterations to convergence 244 setup time was (sec) 0.8900000 now iterating at: 14:03:18 rms-change max change #iterations 5.179185 241.6008 at 10iterations 2.643252 82.89798 at 20iterations 1.353533 41.60199 at 30iterations 0.6954359 21.07099 at 40iterations 0.3558542 10.08450 at 50iterations 0.1824995 4.816927 at 60iterations 9.3589179E-02 2.652629 at 70iterations 4.7965117E-02 1.318976 at 80iterations 2.4609206E-02 0.7656765 at 90iterations 1.2651267E-02 0.3755798 at 100iterations 6.4822142E-03 0.1874647 at 110iterations 3.3226071E-03 9.0587974E-02 at 120iterations finished qdiffx linear iterations at : 14:03:25 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 3.3226071E-03 9.0587974E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 14:03:26 7.719u 0.246s 0:08.75 90.8% 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 14:03:26 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2121 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.364910 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): -21.06800 24.68400 ymin,ymax (A): -8.027000 36.62000 zmin,zma (A): -3.577000 44.03200 x,y,z range (A): 45.75200 44.64700 47.60900 scale (grids/A): 3.364910 object centre (A): 1.808000 14.29650 20.22750 number of atom coordinates read : 2121 total number of charged atoms : 1981 net assigned charge : -4.771990 assigned positive charge : 317.4509 centred at (gu) : 85.27731 91.69966 91.94710 assigned negative charge : -322.2230 centred at (gu) : 85.21352 91.87934 92.52388 start vw surface at 0.1400000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 196648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19063 grid for indexing accessible points = 1.400000 m= 104137 mr = 141782 m= 44487 mr = 86253 m= 13882 mr = 36687 m= 3227 mr = 10912 m= 442 mr = 2454 m= 14 mr = 290 m= 0 mr = 6 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 84453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 15844 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) : 2.243273 object centre at (A) : 1.808000 14.29650 20.22750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0491821E-02 -1.190631 midg,1,midg; midg,igrid,midg -0.2561314 -0.1599420 1,midg,midg; igrid,midg,midg 7.5556777E-02 -0.1041094 gauss-seidel spectral radius is 0.9993239 estimated iterations to convergence 303 setup time was (sec) 2.330000 now iterating at: 14:03:29 rms-change max change #iterations 11.11648 305.2117 at 10iterations 6.547049 121.6826 at 20iterations 3.870492 78.17501 at 30iterations 2.282015 40.02211 at 40iterations 1.345890 23.66254 at 50iterations 0.7931396 12.19083 at 60iterations 0.4665396 7.761843 at 70iterations 0.2754030 4.262186 at 80iterations 0.1618935 2.702235 at 90iterations 9.5336631E-02 1.581105 at 100iterations 5.6071479E-02 0.8997073 at 110iterations 3.2968532E-02 0.5143471 at 120iterations 1.9386342E-02 0.3108482 at 130iterations 1.1428636E-02 0.1832176 at 140iterations 6.7334268E-03 0.1103721 at 150iterations 3.9529195E-03 6.4054489E-02 at 160iterations 2.3266680E-03 3.6081314E-02 at 170iterations 1.3674960E-03 2.1794319E-02 at 180iterations finished qdiffx linear iterations at : 14:03:39 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 1.3674960E-03 2.1794319E-02 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 14:03:40 13.115u 0.202s 0:13.94 95.4% 0+0k 0+0io 0pf+0w