Sun Oct 9 00:04:58 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 Sun Oct 9 2011 at 00:04:58 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 = 2248 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: 0.6395745 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): 0.4799999 53.56700 ymin,ymax (A): 8.077000 51.51500 zmin,zma (A): -7.521000 48.14100 x,y,z range (A): 53.08700 43.43800 55.66200 scale (grids/A): 0.6395745 object centre (A): 27.02350 29.79600 20.31000 number of atom coordinates read : 2248 total number of charged atoms : 2114 net assigned charge : 10.50002 assigned positive charge : 324.6146 centred at (gu) : 89.09228 90.90023 89.32660 assigned negative charge : -314.1151 centred at (gu) : 89.06052 90.82130 89.32755 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6354 nv = 96 ne = 84 npr = 44751 no. pairs analyzed = 44751 no. exposed pairs = 3105 no. arc points = 22020 no. surface atoms = 1030 nbur = 1218 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3215 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2145 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7440 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7385062E-08 1.3008973E-08 midg,1,midg; midg,igrid,midg 6.3929142E-09 2.7003196E-08 1,midg,midg; igrid,midg,midg 1.4523485E-08 1.4893618E-08 gauss-seidel spectral radius is 0.9873127 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 00:04:59 rms-change max change #iterations 0.1284750 19.89419 at 10iterations 1.2639195E-02 1.947765 at 20iterations 1.2353359E-03 0.1932530 at 30iterations 1.2267151E-04 1.8555641E-02 at 40iterations 1.2249699E-05 2.0394325E-03 at 50iterations finished qdiffx linear iterations at : 00:05:01 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.2249699E-05 2.0394325E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 00:05:02 3.398u 0.172s 0:03.84 92.7% 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 Sun Oct 9 2011 at 00:05:02 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 = 2248 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918724 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): 0.4799999 53.56700 ymin,ymax (A): 8.077000 51.51500 zmin,zma (A): -7.521000 48.14100 x,y,z range (A): 53.08700 43.43800 55.66200 scale (grids/A): 1.918724 object centre (A): 27.02350 29.79600 20.31000 number of atom coordinates read : 2248 total number of charged atoms : 2114 net assigned charge : 10.50002 assigned positive charge : 324.6146 centred at (gu) : 87.27655 92.70051 87.97931 assigned negative charge : -314.1151 centred at (gu) : 87.18163 92.46424 87.98275 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 67359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22020 grid for indexing accessible points = 1.400000 m= 24130 mr = 44433 m= 3836 mr = 17066 m= 226 mr = 2231 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 31762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 16650 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) : 0.6395745 object centre at (A) : 27.02350 29.79600 20.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8982617E-02 5.3153861E-02 midg,1,midg; midg,igrid,midg -3.1591898E-03 2.3118636E-02 1,midg,midg; igrid,midg,midg 4.7940724E-02 4.0397964E-02 gauss-seidel spectral radius is 0.9986289 estimated iterations to convergence 214 setup time was (sec) 0.5400000 now iterating at: 00:05:03 rms-change max change #iterations 3.815701 189.9881 at 10iterations 1.774060 71.05278 at 20iterations 0.8272865 29.04744 at 30iterations 0.3845514 12.94442 at 40iterations 0.1799040 6.569834 at 50iterations 8.3858006E-02 2.852695 at 60iterations 3.9000753E-02 1.329468 at 70iterations 1.8259941E-02 0.5787640 at 80iterations 8.5289152E-03 0.3016214 at 90iterations 3.9858161E-03 0.1395297 at 100iterations 1.8579199E-03 6.2787056E-02 at 110iterations 8.6999178E-04 3.1921387E-02 at 120iterations finished qdiffx linear iterations at : 00:05:10 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 8.6999178E-04 3.1921387E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 00:05:10 7.731u 0.223s 0:08.21 96.8% 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 Sun Oct 9 2011 at 00:05:10 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 = 2248 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: 2.878085 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): 0.4799999 53.56700 ymin,ymax (A): 8.077000 51.51500 zmin,zma (A): -7.521000 48.14100 x,y,z range (A): 53.08700 43.43800 55.66200 scale (grids/A): 2.878085 object centre (A): 27.02350 29.79600 20.31000 number of atom coordinates read : 2248 total number of charged atoms : 2114 net assigned charge : 10.50002 assigned positive charge : 324.6146 centred at (gu) : 85.91464 94.05075 86.96910 assigned negative charge : -314.1151 centred at (gu) : 85.77249 93.69640 86.97420 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 155429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22020 grid for indexing accessible points = 1.400000 m= 77154 mr = 108128 m= 28154 mr = 61415 m= 6674 mr = 21889 m= 946 mr = 4688 m= 43 mr = 568 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 71702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 16911 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) : 1.918724 object centre at (A) : 27.02350 29.79600 20.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2063010 0.6694267 midg,1,midg; midg,igrid,midg -2.2369141E-02 0.2268907 1,midg,midg; igrid,midg,midg 0.4204540 0.4183783 gauss-seidel spectral radius is 0.9992599 estimated iterations to convergence 290 setup time was (sec) 1.100000 now iterating at: 00:05:11 rms-change max change #iterations 9.132854 345.5984 at 10iterations 5.376215 133.1498 at 20iterations 3.130359 89.89096 at 30iterations 1.819171 44.42646 at 40iterations 1.056956 23.89846 at 50iterations 0.6091501 11.57156 at 60iterations 0.3520709 7.133394 at 70iterations 0.2029598 4.286434 at 80iterations 0.1170350 2.414345 at 90iterations 6.7148812E-02 1.358381 at 100iterations 3.8697764E-02 0.7226973 at 110iterations 2.2270067E-02 0.4734268 at 120iterations 1.2786582E-02 0.2367172 at 130iterations 7.3329248E-03 0.1345901 at 140iterations 4.2156093E-03 7.8742981E-02 at 150iterations 2.4237104E-03 4.7249794E-02 at 160iterations 1.3910095E-03 2.5897980E-02 at 170iterations 7.9764723E-04 1.5386581E-02 at 180iterations finished qdiffx linear iterations at : 00:05:23 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 7.9764723E-04 1.5386581E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 00:05:23 12.483u 0.202s 0:13.02 97.3% 0+0k 0+0io 0pf+0w