Mon Oct 10 19:32:35 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 19:32:35 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2419 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6004081 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): -11.25800 48.03500 ymin,ymax (A): 60.49900 115.5460 zmin,zma (A): 44.04900 87.68400 x,y,z range (A): 59.29300 55.04701 43.63500 scale (grids/A): 0.6004081 object centre (A): 18.38850 88.02250 65.86650 number of atom coordinates read : 2419 total number of charged atoms : 2280 net assigned charge : 2.8007537E-02 assigned positive charge : 368.4537 centred at (gu) : 87.79125 91.25774 91.37436 assigned negative charge : -368.4265 centred at (gu) : 87.84781 91.35460 91.49617 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5882 nv = 96 ne = 84 npr = 48470 no. pairs analyzed = 48470 no. exposed pairs = 3042 no. arc points = 20896 no. surface atoms = 1019 nbur = 1400 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 3231 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1036025E-09 -5.7981220E-09 midg,1,midg; midg,igrid,midg 2.5537648E-09 -4.4503183E-09 1,midg,midg; igrid,midg,midg 3.4079899E-09 -1.1450416E-09 gauss-seidel spectral radius is 0.9856274 estimated iterations to convergence 68 setup time was (sec) 0.5200000 now iterating at: 19:32:36 rms-change max change #iterations 0.1056590 17.77071 at 10iterations 9.0321777E-03 1.477830 at 20iterations 8.1037730E-04 0.1187096 at 30iterations 8.9823341E-05 1.8176556E-02 at 40iterations 1.7429489E-05 3.7374794E-03 at 50iterations finished qdiffx linear iterations at : 19:32:38 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.7429489E-05 3.7374794E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 19:32:39 3.416u 0.196s 0:04.19 85.9% 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 Mon Oct 10 2011 at 19:32:39 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2419 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 1.801224 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): -11.25800 48.03500 ymin,ymax (A): 60.49900 115.5460 zmin,zma (A): 44.04900 87.68400 x,y,z range (A): 59.29300 55.04701 43.63500 scale (grids/A): 1.801224 object centre (A): 18.38850 88.02250 65.86650 number of atom coordinates read : 2419 total number of charged atoms : 2280 net assigned charge : 2.8007537E-02 assigned positive charge : 368.4537 centred at (gu) : 83.37328 93.77271 94.12234 assigned negative charge : -368.4265 centred at (gu) : 83.54319 94.06361 94.48801 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20896 grid for indexing accessible points = 1.400000 m= 22417 mr = 44582 m= 3081 mr = 16359 m= 132 mr = 1764 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 413 time to turn everything in is 0.4800000 number of dielectric boundary points 26796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 17830 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) : 0.6004081 object centre at (A) : 18.38850 88.02250 65.86650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0470860E-03 -6.1811227E-03 midg,1,midg; midg,igrid,midg 2.2177055E-02 -1.6425442E-02 1,midg,midg; igrid,midg,midg -1.4096269E-02 -1.3216199E-02 gauss-seidel spectral radius is 0.9984538 estimated iterations to convergence 202 setup time was (sec) 0.7700000 now iterating at: 19:32:40 rms-change max change #iterations 3.692647 179.7686 at 10iterations 1.640279 68.04002 at 20iterations 0.7325673 25.34772 at 30iterations 0.3267377 11.27873 at 40iterations 0.1453119 5.098679 at 50iterations 6.4869292E-02 2.612179 at 60iterations 2.8906537E-02 1.005375 at 70iterations 1.2974124E-02 0.4206219 at 80iterations 5.7912790E-03 0.2028084 at 90iterations 2.5822814E-03 9.1461182E-02 at 100iterations 1.1612042E-03 4.0885925E-02 at 110iterations 5.2225601E-04 1.8308640E-02 at 120iterations finished qdiffx linear iterations at : 19:32:47 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 5.2225601E-04 1.8308640E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 19:32:47 7.457u 0.209s 0:07.98 95.8% 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 19:32:47 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2419 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 2.701837 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): -11.25800 48.03500 ymin,ymax (A): 60.49900 115.5460 zmin,zma (A): 44.04900 87.68400 x,y,z range (A): 59.29300 55.04701 43.63500 scale (grids/A): 2.701837 object centre (A): 18.38850 88.02250 65.86650 number of atom coordinates read : 2419 total number of charged atoms : 2280 net assigned charge : 2.8007537E-02 assigned positive charge : 368.4537 centred at (gu) : 80.05979 95.65889 96.18330 assigned negative charge : -368.4265 centred at (gu) : 80.31470 96.09537 96.73192 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 148002 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20896 grid for indexing accessible points = 1.400000 m= 73518 mr = 108317 m= 25395 mr = 59704 m= 5356 mr = 20185 m= 623 mr = 3877 m= 35 mr = 377 m= 0 mr = 15 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1397 time to turn everything in is 1.150000 number of dielectric boundary points 60454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 18236 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) : 1.801224 object centre at (A) : 18.38850 88.02250 65.86650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1654715E-02 -3.6700509E-02 midg,1,midg; midg,igrid,midg 0.3319847 -0.2637796 1,midg,midg; igrid,midg,midg -0.2344127 -4.5854873E-03 gauss-seidel spectral radius is 0.9992031 estimated iterations to convergence 280 setup time was (sec) 1.460000 now iterating at: 19:32:49 rms-change max change #iterations 8.995450 278.7303 at 10iterations 5.178135 114.8096 at 20iterations 2.944088 68.59171 at 30iterations 1.675789 35.95438 at 40iterations 0.9476405 20.68280 at 50iterations 0.5357524 11.14575 at 60iterations 0.3033057 6.400884 at 70iterations 0.1707933 3.362074 at 80iterations 9.6582107E-02 2.094938 at 90iterations 5.4272577E-02 1.319241 at 100iterations 3.0501807E-02 0.6133089 at 110iterations 1.7168347E-02 0.3715143 at 120iterations 9.6747326E-03 0.2303257 at 130iterations 5.4452829E-03 0.1188354 at 140iterations 3.0675430E-03 6.1547995E-02 at 150iterations 1.7298260E-03 3.9330482E-02 at 160iterations 9.7695284E-04 1.9992828E-02 at 170iterations 5.5396074E-04 1.0871887E-02 at 180iterations finished qdiffx linear iterations at : 19:33:00 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 5.5396074E-04 1.0871887E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 19:33:01 12.826u 0.218s 0:13.36 97.5% 0+0k 0+0io 0pf+0w