Sat Oct 8 11:39:00 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 Sat Oct 8 2011 at 11:39:00 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4367 !!! WARNING: HIQ 440 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5637014 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): -27.65300 35.50100 ymin,ymax (A): 38.16500 95.72100 zmin,zma (A): 30.71700 90.31700 x,y,z range (A): 63.15400 57.55600 59.60000 scale (grids/A): 0.5637014 object centre (A): 3.924002 66.94300 60.51700 number of atom coordinates read : 4367 total number of charged atoms : 4207 net assigned charge : -5.485951 assigned positive charge : 657.2845 centred at (gu) : 90.91778 88.67446 89.13084 assigned negative charge : -662.7734 centred at (gu) : 90.80916 88.75608 89.31469 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8809 nv = 96 ne = 84 npr = 92028 no. pairs analyzed = 92028 no. exposed pairs = 4890 no. arc points = 33263 no. surface atoms = 1645 nbur = 2722 mkacc time = 0.2700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 370 mr = 5120 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.5500000 number of dielectric boundary points 4024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3447 ## 444 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 11598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2726259E-09 -3.4608691E-09 midg,1,midg; midg,igrid,midg 1.0935112E-09 -1.6652900E-09 1,midg,midg; igrid,midg,midg -2.2499957E-09 1.6049418E-09 gauss-seidel spectral radius is 0.9838591 estimated iterations to convergence 65 setup time was (sec) 0.8300000 now iterating at: 11:39:01 rms-change max change #iterations 0.1076830 19.39984 at 10iterations 9.3385391E-03 1.244446 at 20iterations 1.8165484E-03 0.2427120 at 30iterations 6.3308759E-04 8.0749512E-02 at 40iterations 2.5121789E-04 3.5331726E-02 at 50iterations finished qdiffx linear iterations at : 11:39:04 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 2.5121789E-04 3.5331726E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 11:39:04 4.255u 0.174s 0:04.71 93.8% 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 Sat Oct 8 2011 at 11:39:04 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4367 !!! WARNING: HIQ 440 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.691104 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): -27.65300 35.50100 ymin,ymax (A): 38.16500 95.72100 zmin,zma (A): 30.71700 90.31700 x,y,z range (A): 63.15400 57.55600 59.60000 scale (grids/A): 1.691104 object centre (A): 3.924002 66.94300 60.51700 number of atom coordinates read : 4367 total number of charged atoms : 4207 net assigned charge : -5.485951 assigned positive charge : 657.2845 centred at (gu) : 92.75195 86.02216 87.39172 assigned negative charge : -662.7734 centred at (gu) : 92.42696 86.26768 87.94380 start vw surface at 0.2400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 97617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33263 grid for indexing accessible points = 1.400000 m= 33875 mr = 70669 m= 4084 mr = 25415 m= 124 mr = 2412 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 5511 time to turn everything in is 0.8500000 number of dielectric boundary points 37184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 321 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 32472 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) : 0.5637014 object centre at (A) : 3.924002 66.94300 60.51700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0152669E-02 -2.6863633E-02 midg,1,midg; midg,igrid,midg 1.9873038E-02 -1.0447226E-02 1,midg,midg; igrid,midg,midg -2.3738418E-02 2.6834469E-02 gauss-seidel spectral radius is 0.9984283 estimated iterations to convergence 200 setup time was (sec) 1.210000 now iterating at: 11:39:06 rms-change max change #iterations 4.505971 172.7650 at 10iterations 1.998467 77.87253 at 20iterations 0.8897725 26.78533 at 30iterations 0.3956999 11.73276 at 40iterations 0.1754907 5.652348 at 50iterations 7.8378141E-02 2.418757 at 60iterations 3.5116881E-02 1.070427 at 70iterations 1.5915990E-02 0.4771742 at 80iterations 7.3713209E-03 0.2210236 at 90iterations 3.5950777E-03 0.1071510 at 100iterations 1.9274539E-03 6.1161041E-02 at 110iterations 1.1561132E-03 3.5259247E-02 at 120iterations finished qdiffx linear iterations at : 11:39:14 total time elapsed so far: 9.070000 # loops : 120 mean,max change (kT/e) : 1.1561132E-03 3.5259247E-02 energy calculations done at 9.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 11:39:14 9.307u 0.206s 0:09.81 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 Sat Oct 8 2011 at 11:39:14 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4367 !!! WARNING: HIQ 440 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.536656 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): -27.65300 35.50100 ymin,ymax (A): 38.16500 95.72100 zmin,zma (A): 30.71700 90.31700 x,y,z range (A): 63.15400 57.55600 59.60000 scale (grids/A): 2.536656 object centre (A): 3.924002 66.94300 60.51700 number of atom coordinates read : 4367 total number of charged atoms : 4207 net assigned charge : -5.485951 assigned positive charge : 657.2845 centred at (gu) : 94.12781 84.03286 86.08719 assigned negative charge : -662.7734 centred at (gu) : 93.64035 84.40152 86.91559 start vw surface at 0.2200000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 226570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33263 grid for indexing accessible points = 1.400000 m= 113379 mr = 171191 m= 37062 mr = 93916 m= 6957 mr = 30187 m= 593 mr = 5092 m= 16 mr = 341 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 18595 time to turn everything in is 2.090000 number of dielectric boundary points 83850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 33631 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) : 1.691104 object centre at (A) : 3.924002 66.94300 60.51700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6901867 -0.3416249 midg,1,midg; midg,igrid,midg 0.3089058 -0.2303351 1,midg,midg; igrid,midg,midg -0.2579591 0.3641924 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 2.490000 now iterating at: 11:39:17 rms-change max change #iterations 11.24598 306.1026 at 10iterations 6.498475 127.9627 at 20iterations 3.732442 68.70503 at 30iterations 2.143110 41.40461 at 40iterations 1.223953 20.60740 at 50iterations 0.7003474 12.17619 at 60iterations 0.3993060 7.521729 at 70iterations 0.2279399 3.756470 at 80iterations 0.1299622 2.183739 at 90iterations 7.4083559E-02 1.398453 at 100iterations 4.2268105E-02 0.6983156 at 110iterations 2.4336636E-02 0.4568653 at 120iterations 1.4077172E-02 0.2427673 at 130iterations 8.2971472E-03 0.1439743 at 140iterations 5.0396649E-03 9.3827248E-02 at 150iterations 3.2105353E-03 6.1096191E-02 at 160iterations 2.1732105E-03 3.7826538E-02 at 170iterations 1.5682121E-03 3.0675888E-02 at 180iterations finished qdiffx linear iterations at : 11:39:29 total time elapsed so far: 14.86000 # loops : 180 mean,max change (kT/e) : 1.5682121E-03 3.0675888E-02 energy calculations done at 14.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.09000 DelPhi exited at 11:39:30 15.091u 0.248s 0:15.62 98.1% 0+0k 0+0io 0pf+0w