Tue Oct 11 08:21:31 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 Tue Oct 11 2011 at 08:21:31 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1173 !!! WARNING: HIT 60 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7523245 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): -6.923000 31.91900 ymin,ymax (A): 1.065000 39.89000 zmin,zma (A): -1.541000 45.77900 x,y,z range (A): 38.84200 38.82500 47.32000 scale (grids/A): 0.7523245 object centre (A): 12.49800 20.47750 22.11900 number of atom coordinates read : 1173 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 177.7651 centred at (gu) : 88.80171 89.36252 88.32572 assigned negative charge : -172.2511 centred at (gu) : 88.48622 89.34712 88.34366 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4453 nv = 96 ne = 84 npr = 23117 no. pairs analyzed = 23117 no. exposed pairs = 1520 no. arc points = 11060 no. surface atoms = 517 nbur = 656 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 2274 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2400000 number of dielectric boundary points 2407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 847 ## 68 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 4579 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9144589E-07 8.6993808E-08 midg,1,midg; midg,igrid,midg 1.3246344E-07 1.2478557E-07 1,midg,midg; igrid,midg,midg -1.2478576E-07 2.7486911E-07 gauss-seidel spectral radius is 0.9906932 estimated iterations to convergence 84 setup time was (sec) 0.5300000 now iterating at: 08:21:32 rms-change max change #iterations 0.1931071 40.09430 at 10iterations 2.6387043E-02 4.802162 at 20iterations 3.5155239E-03 0.5766773 at 30iterations 4.8213135E-04 7.8094482E-02 at 40iterations 6.7507266E-05 1.0652542E-02 at 50iterations finished qdiffx linear iterations at : 08:21:35 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 6.7507266E-05 1.0652542E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 08:21:36 4.377u 0.305s 0:05.10 91.5% 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 Tue Oct 11 2011 at 08:21:36 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1173 !!! WARNING: HIT 60 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: 2.256974 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): -6.923000 31.91900 ymin,ymax (A): 1.065000 39.89000 zmin,zma (A): -1.541000 45.77900 x,y,z range (A): 38.84200 38.82500 47.32000 scale (grids/A): 2.256974 object centre (A): 12.49800 20.47750 22.11900 number of atom coordinates read : 1173 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 177.7651 centred at (gu) : 86.40512 88.08776 84.97734 assigned negative charge : -172.2511 centred at (gu) : 85.45882 88.04162 85.03108 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 46468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11060 grid for indexing accessible points = 1.400000 m= 17038 mr = 30176 m= 3187 mr = 12566 m= 291 mr = 2131 m= 16 mr = 137 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 194 time to turn everything in is 0.5400000 number of dielectric boundary points 21988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 8452 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) : 0.7523245 object centre at (A) : 12.49800 20.47750 22.11900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9102055E-02 4.8228223E-03 midg,1,midg; midg,igrid,midg 4.0629607E-02 3.2223735E-02 1,midg,midg; igrid,midg,midg -3.2934964E-02 4.8058417E-02 gauss-seidel spectral radius is 0.9988633 estimated iterations to convergence 235 setup time was (sec) 0.9300000 now iterating at: 08:21:37 rms-change max change #iterations 3.782959 229.9874 at 10iterations 1.877890 74.14284 at 20iterations 0.9395774 37.36541 at 30iterations 0.4694133 18.59202 at 40iterations 0.2341999 8.407074 at 50iterations 0.1173951 4.971920 at 60iterations 5.8234718E-02 2.145599 at 70iterations 2.9180916E-02 1.075403 at 80iterations 1.4586722E-02 0.5509892 at 90iterations 7.2646188E-03 0.2772961 at 100iterations 3.6257945E-03 0.1320105 at 110iterations 1.8212292E-03 6.6261292E-02 at 120iterations finished qdiffx linear iterations at : 08:21:46 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 1.8212292E-03 6.6261292E-02 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.43000 DelPhi exited at 08:21:47 10.429u 0.352s 0:11.23 95.9% 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 Tue Oct 11 2011 at 08:21:47 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1173 !!! WARNING: HIT 60 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.385460 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): -6.923000 31.91900 ymin,ymax (A): 1.065000 39.89000 zmin,zma (A): -1.541000 45.77900 x,y,z range (A): 38.84200 38.82500 47.32000 scale (grids/A): 3.385460 object centre (A): 12.49800 20.47750 22.11900 number of atom coordinates read : 1173 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 177.7651 centred at (gu) : 84.60771 87.13161 82.46602 assigned negative charge : -172.2511 centred at (gu) : 83.18829 87.06245 82.54670 start vw surface at 0.1400000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 106845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11060 grid for indexing accessible points = 1.400000 m= 53038 mr = 72912 m= 21426 mr = 42977 m= 6028 mr = 17504 m= 1171 mr = 4673 m= 160 mr = 844 m= 5 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 531 time to turn everything in is 1.510000 number of dielectric boundary points 49678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 8488 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) : 2.256974 object centre at (A) : 12.49800 20.47750 22.11900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3459991 5.0585713E-02 midg,1,midg; midg,igrid,midg 0.3383709 0.2699187 1,midg,midg; igrid,midg,midg -0.2653993 0.3428968 gauss-seidel spectral radius is 0.9992992 estimated iterations to convergence 298 setup time was (sec) 1.920000 now iterating at: 08:21:49 rms-change max change #iterations 8.178067 292.6281 at 10iterations 4.767420 114.2540 at 20iterations 2.772222 65.15851 at 30iterations 1.614189 38.95453 at 40iterations 0.9399254 19.37545 at 50iterations 0.5464891 11.72708 at 60iterations 0.3171903 7.002960 at 70iterations 0.1844711 3.808121 at 80iterations 0.1073577 2.215289 at 90iterations 6.2447149E-02 1.312224 at 100iterations 3.6356229E-02 0.8249588 at 110iterations 2.1067830E-02 0.4132662 at 120iterations 1.2242108E-02 0.2677364 at 130iterations 7.1264533E-03 0.1493981 at 140iterations 4.1468181E-03 8.1752896E-02 at 150iterations 2.4098605E-03 5.1706791E-02 at 160iterations 1.4026155E-03 2.9541016E-02 at 170iterations 8.1744412E-04 1.9504547E-02 at 180iterations finished qdiffx linear iterations at : 08:22:04 total time elapsed so far: 16.55000 # loops : 180 mean,max change (kT/e) : 8.1744412E-04 1.9504547E-02 energy calculations done at 16.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.80000 DelPhi exited at 08:22:05 16.806u 0.374s 0:17.73 96.8% 0+0k 0+0io 0pf+0w