Sat Oct 8 20:24:33 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 Sat Oct 8 2011 at 20:24:33 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 = 2579 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: 0.6258900 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): -38.69800 10.06200 ymin,ymax (A): -13.99000 33.58300 zmin,zma (A): -44.65500 12.22400 x,y,z range (A): 48.76000 47.57300 56.87900 scale (grids/A): 0.6258900 object centre (A): -14.31800 9.796500 -16.21550 number of atom coordinates read : 2579 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 91.60442 89.44757 90.28267 assigned negative charge : -386.5045 centred at (gu) : 91.70487 89.47707 90.37583 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6593 nv = 96 ne = 84 npr = 54128 no. pairs analyzed = 54128 no. exposed pairs = 2962 no. arc points = 21264 no. surface atoms = 990 nbur = 1589 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3711 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 85 time to turn everything in is 0.2000000 number of dielectric boundary points 3170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2154 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8203 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0079785E-08 -4.1028878E-09 midg,1,midg; midg,igrid,midg 6.5528893E-09 1.0839214E-09 1,midg,midg; igrid,midg,midg 7.9643554E-09 -6.4404637E-09 gauss-seidel spectral radius is 0.9867715 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 20:24:34 rms-change max change #iterations 0.1309402 19.80772 at 10iterations 1.2320591E-02 1.890491 at 20iterations 1.1811664E-03 0.1883292 at 30iterations 1.1095180E-04 1.6762733E-02 at 40iterations 1.0569024E-05 1.4953613E-03 at 50iterations finished qdiffx linear iterations at : 20:24:37 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.0569024E-05 1.4953613E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 20:24:38 3.639u 0.182s 0:04.12 92.4% 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 20:24:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 1.877670 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): -38.69800 10.06200 ymin,ymax (A): -13.99000 33.58300 zmin,zma (A): -44.65500 12.22400 x,y,z range (A): 48.76000 47.57300 56.87900 scale (grids/A): 1.877670 object centre (A): -14.31800 9.796500 -16.21550 number of atom coordinates read : 2579 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 94.81252 88.34219 90.84750 assigned negative charge : -386.5045 centred at (gu) : 95.11436 88.43113 91.12744 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21264 grid for indexing accessible points = 1.400000 m= 24458 mr = 50425 m= 3516 mr = 18168 m= 166 mr = 2237 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6537 time to turn everything in is 0.3500000 number of dielectric boundary points 29081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19283 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) : 0.6258900 object centre at (A) : -14.31800 9.796500 -16.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7239669E-02 -5.5645052E-03 midg,1,midg; midg,igrid,midg 1.0555211E-02 -1.0741138E-04 1,midg,midg; igrid,midg,midg 3.7883744E-02 -5.6086709E-03 gauss-seidel spectral radius is 0.9985899 estimated iterations to convergence 211 setup time was (sec) 0.5800000 now iterating at: 20:24:38 rms-change max change #iterations 4.083033 167.4663 at 10iterations 1.879071 68.40551 at 20iterations 0.8694560 28.49964 at 30iterations 0.4019037 13.62804 at 40iterations 0.1869321 6.922110 at 50iterations 8.6235002E-02 2.646988 at 60iterations 3.9873887E-02 1.267085 at 70iterations 1.8534474E-02 0.5488863 at 80iterations 8.5547650E-03 0.2629105 at 90iterations 3.9600763E-03 0.1263313 at 100iterations 1.8305125E-03 6.2777519E-02 at 110iterations 8.4931945E-04 2.8419495E-02 at 120iterations finished qdiffx linear iterations at : 20:24:46 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 8.4931945E-04 2.8419495E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 20:24:46 8.285u 0.238s 0:08.81 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 Sat Oct 8 2011 at 20:24:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 2.816505 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): -38.69800 10.06200 ymin,ymax (A): -13.99000 33.58300 zmin,zma (A): -44.65500 12.22400 x,y,z range (A): 48.76000 47.57300 56.87900 scale (grids/A): 2.816505 object centre (A): -14.31800 9.796500 -16.21550 number of atom coordinates read : 2579 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 97.21873 87.51315 91.27112 assigned negative charge : -386.5045 centred at (gu) : 97.67138 87.64655 91.69095 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 166052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21264 grid for indexing accessible points = 1.400000 m= 81641 mr = 121780 m= 27587 mr = 67358 m= 6322 mr = 22198 m= 812 mr = 4894 m= 29 mr = 544 m= 0 mr = 5 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 22423 time to turn everything in is 0.9100000 number of dielectric boundary points 65664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19623 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) : 1.877670 object centre at (A) : -14.31800 9.796500 -16.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1184622 7.9125136E-02 midg,1,midg; midg,igrid,midg 0.1324947 -1.5625466E-02 1,midg,midg; igrid,midg,midg 0.4836726 -5.7729498E-02 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 1.180000 now iterating at: 20:24:48 rms-change max change #iterations 9.484241 347.3290 at 10iterations 5.423263 111.6950 at 20iterations 3.079872 61.03698 at 30iterations 1.749913 32.05018 at 40iterations 0.9952351 17.30442 at 50iterations 0.5643729 10.44152 at 60iterations 0.3214052 6.614497 at 70iterations 0.1828648 3.853543 at 80iterations 0.1040047 2.095486 at 90iterations 5.9161119E-02 1.056534 at 100iterations 3.3578735E-02 0.5977058 at 110iterations 1.9111166E-02 0.3777161 at 120iterations 1.0863478E-02 0.2042122 at 130iterations 6.1859516E-03 0.1097345 at 140iterations 3.5133348E-03 6.1174393E-02 at 150iterations 1.9976173E-03 3.6251068E-02 at 160iterations 1.1380995E-03 2.0421028E-02 at 170iterations 6.4741197E-04 1.1284828E-02 at 180iterations finished qdiffx linear iterations at : 20:25:00 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 6.4741197E-04 1.1284828E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.79000 DelPhi exited at 20:25:01 13.787u 0.254s 0:14.31 98.0% 0+0k 0+0io 0pf+0w