Wed Feb 1 08:56:49 PST 2012 #!/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 Wed Feb 1 2012 at 08:56:49 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2212 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: 0.6870332 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 0.6870332 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2212 total number of charged atoms : 2070 net assigned charge : 3.000011 assigned positive charge : 329.2835 centred at (gu) : 88.63007 89.00397 90.29876 assigned negative charge : -326.2838 centred at (gu) : 88.50322 89.05289 90.31750 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7233 nv = 96 ne = 84 npr = 44250 no. pairs analyzed = 44250 no. exposed pairs = 3045 no. arc points = 21287 no. surface atoms = 1028 nbur = 1184 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 3719 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1895 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0659874E-08 1.0375864E-08 midg,1,midg; midg,igrid,midg 3.8553257E-08 1.5539688E-10 1,midg,midg; igrid,midg,midg -3.4313913E-08 4.2787612E-08 gauss-seidel spectral radius is 0.9889877 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 08:56:50 rms-change max change #iterations 0.1835666 27.86543 at 10iterations 2.0976659E-02 2.911405 at 20iterations 2.4002616E-03 0.3321705 at 30iterations 2.8387795E-04 3.5943985E-02 at 40iterations 3.6033874E-05 6.1759949E-03 at 50iterations finished qdiffx linear iterations at : 08:56:53 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.6033874E-05 6.1759949E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 08:56:53 3.450u 0.232s 0:04.00 92.0% 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 Wed Feb 1 2012 at 08:56:53 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2212 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: 2.061100 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 2.061100 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2212 total number of charged atoms : 2070 net assigned charge : 3.000011 assigned positive charge : 329.2835 centred at (gu) : 85.88992 87.01157 90.89574 assigned negative charge : -326.2838 centred at (gu) : 85.50968 87.15843 90.95237 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 28129 mr = 50951 m= 5586 mr = 20085 m= 485 mr = 3611 m= 19 mr = 251 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 35644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 16412 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) : 0.6870332 object centre at (A) : 16.34250 -28.09450 0.2924995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2580580E-02 2.2695843E-02 midg,1,midg; midg,igrid,midg 2.5004605E-02 -3.5622030E-02 1,midg,midg; igrid,midg,midg -1.3493841E-02 2.5565606E-02 gauss-seidel spectral radius is 0.9988047 estimated iterations to convergence 229 setup time was (sec) 0.6100000 now iterating at: 08:56:54 rms-change max change #iterations 4.524269 184.8578 at 10iterations 2.209453 72.46293 at 20iterations 1.085855 34.97570 at 30iterations 0.5338269 15.60560 at 40iterations 0.2622350 7.916278 at 50iterations 0.1285083 4.288666 at 60iterations 6.3196488E-02 1.912212 at 70iterations 3.1004336E-02 0.9652860 at 80iterations 1.5267700E-02 0.4349337 at 90iterations 7.4981172E-03 0.2302437 at 100iterations 3.6847927E-03 0.1137466 at 110iterations 1.8140497E-03 5.6209564E-02 at 120iterations finished qdiffx linear iterations at : 08:57:02 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 1.8140497E-03 5.6209564E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 08:57:02 8.042u 0.321s 0:08.66 96.5% 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 Wed Feb 1 2012 at 08:57:02 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2212 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: 3.091649 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 3.091649 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2212 total number of charged atoms : 2070 net assigned charge : 3.000011 assigned positive charge : 329.2835 centred at (gu) : 83.83490 85.51737 91.34367 assigned negative charge : -326.2838 centred at (gu) : 83.26443 85.73758 91.42853 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 176333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 87842 mr = 124238 m= 35138 mr = 69978 m= 10359 mr = 27917 m= 2046 mr = 7865 m= 260 mr = 1471 m= 13 mr = 182 m= 0 mr = 4 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 80336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 16560 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) : 2.061100 object centre at (A) : 16.34250 -28.09450 0.2924995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7195667 0.1996875 midg,1,midg; midg,igrid,midg 0.1806889 -0.5210487 1,midg,midg; igrid,midg,midg -7.2177380E-02 0.2583511 gauss-seidel spectral radius is 0.9993078 estimated iterations to convergence 300 setup time was (sec) 1.420000 now iterating at: 08:57:04 rms-change max change #iterations 10.29184 469.6904 at 10iterations 6.136061 134.3790 at 20iterations 3.641131 77.60885 at 30iterations 2.159968 42.23466 at 40iterations 1.276099 23.56931 at 50iterations 0.7525082 13.15571 at 60iterations 0.4428689 8.162300 at 70iterations 0.2600375 5.218888 at 80iterations 0.1529246 3.077034 at 90iterations 8.9582413E-02 1.782769 at 100iterations 5.2671339E-02 0.9648533 at 110iterations 3.0830495E-02 0.5739813 at 120iterations 1.8070262E-02 0.3092003 at 130iterations 1.0570834E-02 0.1817741 at 140iterations 6.1953296E-03 0.1131668 at 150iterations 3.6291967E-03 6.5311432E-02 at 160iterations 2.1301345E-03 3.7193298E-02 at 170iterations 1.2428774E-03 2.2504807E-02 at 180iterations finished qdiffx linear iterations at : 08:57:16 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.2428774E-03 2.2504807E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 08:57:16 13.279u 0.441s 0:14.27 96.0% 0+0k 0+0io 0pf+0w