Mon Oct 10 09:18:34 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 09:18:34 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 !!! WARNING: HIT 187 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6057306 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): -18.22200 36.83200 ymin,ymax (A): -62.99500 -4.223000 zmin,zma (A): -0.8349999 52.60100 x,y,z range (A): 55.05400 58.77200 53.43600 scale (grids/A): 0.6057306 object centre (A): 9.304998 -33.60900 25.88300 number of atom coordinates read : 2788 total number of charged atoms : 2636 net assigned charge : 2.014008 assigned positive charge : 407.0490 centred at (gu) : 89.16077 89.48155 89.33787 assigned negative charge : -405.0354 centred at (gu) : 89.32776 89.41422 89.25665 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7015 nv = 96 ne = 84 npr = 54314 no. pairs analyzed = 54314 no. exposed pairs = 4258 no. arc points = 30429 no. surface atoms = 1399 nbur = 1389 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 406 mr = 3135 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2920 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8555 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1533403E-09 4.0226307E-09 midg,1,midg; midg,igrid,midg -2.3257716E-09 3.6042742E-09 1,midg,midg; igrid,midg,midg 1.0242731E-08 -5.5243827E-09 gauss-seidel spectral radius is 0.9859278 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 09:18:34 rms-change max change #iterations 0.1151385 20.30465 at 10iterations 9.8489337E-03 1.555679 at 20iterations 8.5208484E-04 0.1431923 at 30iterations 7.4918265E-05 1.0749817E-02 at 40iterations 6.5640252E-06 1.3179779E-03 at 50iterations finished qdiffx linear iterations at : 09:18:37 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 6.5640252E-06 1.3179779E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 09:18:38 3.413u 0.182s 0:03.87 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 Mon Oct 10 2011 at 09:18:38 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 !!! WARNING: HIT 187 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.817192 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): -18.22200 36.83200 ymin,ymax (A): -62.99500 -4.223000 zmin,zma (A): -0.8349999 52.60100 x,y,z range (A): 55.05400 58.77200 53.43600 scale (grids/A): 1.817192 object centre (A): 9.304998 -33.60900 25.88300 number of atom coordinates read : 2788 total number of charged atoms : 2636 net assigned charge : 2.014008 assigned positive charge : 407.0490 centred at (gu) : 87.48196 88.44424 88.01320 assigned negative charge : -405.0354 centred at (gu) : 87.98302 88.24252 87.76974 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30429 grid for indexing accessible points = 1.400000 m= 24929 mr = 46227 m= 3593 mr = 16030 m= 154 mr = 1659 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.3800000 number of dielectric boundary points 39433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 210 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20632 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) : 0.6057306 object centre at (A) : 9.304998 -33.60900 25.88300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3582389E-03 -1.0804474E-02 midg,1,midg; midg,igrid,midg 3.0219400E-02 3.1004332E-02 1,midg,midg; igrid,midg,midg 1.7178239E-02 -3.0357579E-03 gauss-seidel spectral radius is 0.9985496 estimated iterations to convergence 208 setup time was (sec) 0.6000000 now iterating at: 09:18:38 rms-change max change #iterations 4.005949 155.7236 at 10iterations 1.819240 79.44220 at 20iterations 0.8328294 31.28860 at 30iterations 0.3796188 14.62959 at 40iterations 0.1732170 5.504433 at 50iterations 7.9167716E-02 2.673354 at 60iterations 3.6127865E-02 1.293659 at 70iterations 1.6477976E-02 0.5507278 at 80iterations 7.5274236E-03 0.2398739 at 90iterations 3.4345123E-03 0.1066628 at 100iterations 1.5658640E-03 5.0390244E-02 at 110iterations 7.1623729E-04 2.5568008E-02 at 120iterations finished qdiffx linear iterations at : 09:18:46 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 7.1623729E-04 2.5568008E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 09:18:46 7.895u 0.195s 0:08.46 95.5% 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 Mon Oct 10 2011 at 09:18:46 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 !!! WARNING: HIT 187 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.725788 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): -18.22200 36.83200 ymin,ymax (A): -62.99500 -4.223000 zmin,zma (A): -0.8349999 52.60100 x,y,z range (A): 55.05400 58.77200 53.43600 scale (grids/A): 2.725788 object centre (A): 9.304998 -33.60900 25.88300 number of atom coordinates read : 2788 total number of charged atoms : 2636 net assigned charge : 2.014008 assigned positive charge : 407.0490 centred at (gu) : 86.22284 87.66629 87.01977 assigned negative charge : -405.0354 centred at (gu) : 86.97439 87.36364 86.65444 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 172229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30429 grid for indexing accessible points = 1.400000 m= 80582 mr = 113696 m= 27698 mr = 60723 m= 6004 mr = 19913 m= 643 mr = 3648 m= 18 mr = 271 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 550 time to turn everything in is 0.9500000 number of dielectric boundary points 88923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 21083 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) : 1.817192 object centre at (A) : 9.304998 -33.60900 25.88300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4214267E-02 -0.1315729 midg,1,midg; midg,igrid,midg 0.5134618 0.3480071 1,midg,midg; igrid,midg,midg 0.1623819 -1.0067996E-02 gauss-seidel spectral radius is 0.9992656 estimated iterations to convergence 291 setup time was (sec) 1.200000 now iterating at: 09:18:47 rms-change max change #iterations 9.906154 320.5038 at 10iterations 5.918910 162.3949 at 20iterations 3.499616 85.52979 at 30iterations 2.057240 55.57099 at 40iterations 1.201705 27.67108 at 50iterations 0.7011840 16.08506 at 60iterations 0.4072779 9.119345 at 70iterations 0.2359177 5.712722 at 80iterations 0.1369261 3.414339 at 90iterations 7.9201296E-02 1.662779 at 100iterations 4.5759685E-02 0.9181544 at 110iterations 2.6494883E-02 0.6545715 at 120iterations 1.5281382E-02 0.3420601 at 130iterations 8.8092191E-03 0.1773441 at 140iterations 5.0787712E-03 9.5470428E-02 at 150iterations 2.9236858E-03 5.8273315E-02 at 160iterations 1.6865898E-03 3.2705307E-02 at 170iterations 9.7087974E-04 1.8753052E-02 at 180iterations finished qdiffx linear iterations at : 09:18:59 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 9.7087974E-04 1.8753052E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 09:19:00 12.916u 0.220s 0:13.47 97.4% 0+0k 0+0io 0pf+0w