Sat Oct 15 14:34:55 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 Sat Oct 15 2011 at 14:34:55 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 = 2858 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: 0.6176267 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): -9.017000 48.62300 ymin,ymax (A): -7.742000 38.96600 zmin,zma (A): -0.3270000 55.36900 x,y,z range (A): 57.64000 46.70800 55.69600 scale (grids/A): 0.6176267 object centre (A): 19.80300 15.61200 27.52100 number of atom coordinates read : 2858 total number of charged atoms : 2717 net assigned charge : -2.499973 assigned positive charge : 428.6222 centred at (gu) : 89.24271 89.59830 89.01125 assigned negative charge : -431.1232 centred at (gu) : 89.16071 89.52917 88.98798 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7341 nv = 96 ne = 84 npr = 57207 no. pairs analyzed = 57207 no. exposed pairs = 3729 no. arc points = 26643 no. surface atoms = 1255 nbur = 1603 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3822 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3000000 number of dielectric boundary points 3827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2680 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2054542E-09 -1.6231902E-10 midg,1,midg; midg,igrid,midg -7.1853936E-09 2.6794660E-09 1,midg,midg; igrid,midg,midg -8.8488479E-09 3.2023140E-09 gauss-seidel spectral radius is 0.9864545 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 14:34:57 rms-change max change #iterations 0.1271099 18.47155 at 10iterations 1.1653187E-02 1.615475 at 20iterations 1.0728227E-03 0.1424198 at 30iterations 9.7477001E-05 1.4214307E-02 at 40iterations 8.8800562E-06 1.3542175E-03 at 50iterations finished qdiffx linear iterations at : 14:35:04 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 8.8800562E-06 1.3542175E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:35:08 3.345u 0.185s 0:13.07 26.9% 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 Sat Oct 15 2011 at 14:35:10 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 = 2858 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: 1.852880 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): -9.017000 48.62300 ymin,ymax (A): -7.742000 38.96600 zmin,zma (A): -0.3270000 55.36900 x,y,z range (A): 57.64000 46.70800 55.69600 scale (grids/A): 1.852880 object centre (A): 19.80300 15.61200 27.52100 number of atom coordinates read : 2858 total number of charged atoms : 2717 net assigned charge : -2.499973 assigned positive charge : 428.6222 centred at (gu) : 87.72729 88.79414 87.03297 assigned negative charge : -431.1232 centred at (gu) : 87.48196 88.58721 86.96379 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 79729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26643 grid for indexing accessible points = 1.400000 m= 26604 mr = 53969 m= 3456 mr = 18704 m= 152 mr = 1897 m= 0 mr = 33 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1324 time to turn everything in is 0.5200000 number of dielectric boundary points 35338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 215 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21303 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) : 0.6176267 object centre at (A) : 19.80300 15.61200 27.52100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0885837E-02 7.3352717E-03 midg,1,midg; midg,igrid,midg -1.8767918E-02 -3.0913192E-04 1,midg,midg; igrid,midg,midg -5.2317534E-02 2.3945319E-02 gauss-seidel spectral radius is 0.9985906 estimated iterations to convergence 211 setup time was (sec) 0.7900000 now iterating at: 14:35:15 rms-change max change #iterations 4.237331 221.3007 at 10iterations 1.960525 72.54110 at 20iterations 0.9042856 31.84036 at 30iterations 0.4179554 15.18791 at 40iterations 0.1931161 6.520400 at 50iterations 8.9213677E-02 2.828617 at 60iterations 4.1278325E-02 1.230355 at 70iterations 1.9103834E-02 0.6025848 at 80iterations 8.8533806E-03 0.2965927 at 90iterations 4.0890006E-03 0.1284666 at 100iterations 1.8901981E-03 6.0148239E-02 at 110iterations 8.7468605E-04 2.5566101E-02 at 120iterations finished qdiffx linear iterations at : 14:35:37 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 8.7468605E-04 2.5566101E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 14:35:39 7.436u 0.163s 0:28.80 26.3% 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 Sat Oct 15 2011 at 14:35:43 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 = 2858 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: 2.779320 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): -9.017000 48.62300 ymin,ymax (A): -7.742000 38.96600 zmin,zma (A): -0.3270000 55.36900 x,y,z range (A): 57.64000 46.70800 55.69600 scale (grids/A): 2.779320 object centre (A): 19.80300 15.61200 27.52100 number of atom coordinates read : 2858 total number of charged atoms : 2717 net assigned charge : -2.499973 assigned positive charge : 428.6222 centred at (gu) : 86.59077 88.19112 85.54909 assigned negative charge : -431.1232 centred at (gu) : 86.22272 87.88084 85.44556 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 184508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26643 grid for indexing accessible points = 1.400000 m= 88236 mr = 131392 m= 29035 mr = 70490 m= 5965 mr = 22442 m= 632 mr = 4079 m= 31 mr = 343 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 4431 time to turn everything in is 1.340000 number of dielectric boundary points 79656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 21735 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) : 1.852880 object centre at (A) : 19.80300 15.61200 27.52100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1792101 -8.5918665E-02 midg,1,midg; midg,igrid,midg -0.1896186 -2.6230134E-02 1,midg,midg; igrid,midg,midg -0.6158607 0.3516231 gauss-seidel spectral radius is 0.9992651 estimated iterations to convergence 291 setup time was (sec) 1.620000 now iterating at: 14:35:50 rms-change max change #iterations 10.20202 271.5511 at 10iterations 6.040119 140.7319 at 20iterations 3.542244 78.30444 at 30iterations 2.063418 48.50805 at 40iterations 1.200472 29.50512 at 50iterations 0.6975158 17.00854 at 60iterations 0.4033559 10.24681 at 70iterations 0.2334197 4.896490 at 80iterations 0.1348381 2.872194 at 90iterations 7.8041308E-02 1.579011 at 100iterations 4.4964913E-02 0.8054025 at 110iterations 2.5954291E-02 0.4874210 at 120iterations 1.4938600E-02 0.2894907 at 130iterations 8.6162221E-03 0.2082577 at 140iterations 4.9599698E-03 9.3273163E-02 at 150iterations 2.8585545E-03 5.0724506E-02 at 160iterations 1.6460087E-03 2.8350830E-02 at 170iterations 9.4746583E-04 1.7612457E-02 at 180iterations finished qdiffx linear iterations at : 14:36:19 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 9.4746583E-04 1.7612457E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 14:36:22 11.507u 0.170s 0:39.42 29.6% 0+0k 0+0io 0pf+0w