Sun Oct 9 07:53:27 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 Sun Oct 9 2011 at 07:53:27 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 0.7191338 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): 1.772000 48.14100 ymin,ymax (A): -16.37600 33.12800 zmin,zma (A): -4.669000 34.87700 x,y,z range (A): 46.36900 49.50400 39.54600 scale (grids/A): 0.7191338 object centre (A): 24.95650 8.376001 15.10400 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 90.00736 90.70414 90.80458 assigned negative charge : -327.3089 centred at (gu) : 89.89024 90.79561 90.94440 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7689 nv = 96 ne = 84 npr = 46060 no. pairs analyzed = 46060 no. exposed pairs = 2768 no. arc points = 19330 no. surface atoms = 934 nbur = 1286 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 535 mr = 4300 m= 5 mr = 120 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 104 time to turn everything in is 0.3200000 number of dielectric boundary points 3810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1800 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8609 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3742384E-07 -3.2515356E-08 midg,1,midg; midg,igrid,midg 1.1249631E-07 6.3088432E-09 1,midg,midg; igrid,midg,midg -1.1459558E-08 1.4562416E-07 gauss-seidel spectral radius is 0.9899344 estimated iterations to convergence 81 setup time was (sec) 0.6000000 now iterating at: 07:53:28 rms-change max change #iterations 0.2190563 29.67841 at 10iterations 2.8005242E-02 4.034645 at 20iterations 3.5276392E-03 0.5540514 at 30iterations 4.5117160E-04 6.0625076E-02 at 40iterations 5.8254696E-05 7.6370239E-03 at 50iterations finished qdiffx linear iterations at : 07:53:31 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 5.8254696E-05 7.6370239E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 07:53:32 4.101u 0.254s 0:04.63 93.9% 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 Sun Oct 9 2011 at 07:53:32 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 2.157401 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): 1.772000 48.14100 ymin,ymax (A): -16.37600 33.12800 zmin,zma (A): -4.669000 34.87700 x,y,z range (A): 46.36900 49.50400 39.54600 scale (grids/A): 2.157401 object centre (A): 24.95650 8.376001 15.10400 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 90.02186 92.11221 92.41354 assigned negative charge : -327.3089 centred at (gu) : 89.67072 92.38673 92.83289 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 80915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19330 grid for indexing accessible points = 1.400000 m= 32220 mr = 55900 m= 6845 mr = 24502 m= 793 mr = 4816 m= 41 mr = 439 m= 0 mr = 12 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2725 time to turn everything in is 0.7800000 number of dielectric boundary points 35145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 16580 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) : 0.7191338 object centre at (A) : 24.95650 8.376001 15.10400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2635911E-02 6.5733893E-03 midg,1,midg; midg,igrid,midg 4.2659994E-02 3.3494633E-02 1,midg,midg; igrid,midg,midg -1.5241187E-02 4.6713851E-02 gauss-seidel spectral radius is 0.9988775 estimated iterations to convergence 236 setup time was (sec) 1.090000 now iterating at: 07:53:33 rms-change max change #iterations 4.948481 250.9615 at 10iterations 2.484494 83.30866 at 20iterations 1.248064 38.86832 at 30iterations 0.6268866 20.44620 at 40iterations 0.3140133 8.657168 at 50iterations 0.1580134 4.628708 at 60iterations 7.9363331E-02 2.260349 at 70iterations 3.9924309E-02 1.065605 at 80iterations 1.9990182E-02 0.5759888 at 90iterations 1.0036629E-02 0.2733688 at 100iterations 5.0717955E-03 0.1576233 at 110iterations 2.5437402E-03 7.2156906E-02 at 120iterations finished qdiffx linear iterations at : 07:53:42 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 2.5437402E-03 7.2156906E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 07:53:42 9.648u 0.270s 0:10.20 97.1% 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 Sun Oct 9 2011 at 07:53:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 3.236102 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): 1.772000 48.14100 ymin,ymax (A): -16.37600 33.12800 zmin,zma (A): -4.669000 34.87700 x,y,z range (A): 46.36900 49.50400 39.54600 scale (grids/A): 3.236102 object centre (A): 24.95650 8.376001 15.10400 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 90.03266 93.16822 93.62023 assigned negative charge : -327.3089 centred at (gu) : 89.50604 93.58006 94.24925 start vw surface at 0.1500000 fill in re-entrant regions at 1.090000 boundary points on vw surface= 186603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19330 grid for indexing accessible points = 1.400000 m= 98671 mr = 134953 m= 42315 mr = 81829 m= 13397 mr = 35270 m= 3193 mr = 10630 m= 509 mr = 2441 m= 45 mr = 357 m= 0 mr = 13 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 8748 time to turn everything in is 2.420000 number of dielectric boundary points 79240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.590000 number of grid points assigned charge 16664 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) : 2.157401 object centre at (A) : 24.95650 8.376001 15.10400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6571912 8.0206543E-02 midg,1,midg; midg,igrid,midg 0.2852571 0.3531295 1,midg,midg; igrid,midg,midg -5.4640867E-02 0.3079293 gauss-seidel spectral radius is 0.9993006 estimated iterations to convergence 298 setup time was (sec) 2.760000 now iterating at: 07:53:45 rms-change max change #iterations 10.72430 386.9105 at 10iterations 6.259229 136.3499 at 20iterations 3.654839 59.48730 at 30iterations 2.131569 37.23339 at 40iterations 1.245664 23.63747 at 50iterations 0.7271978 12.66703 at 60iterations 0.4238926 6.789951 at 70iterations 0.2473419 4.032369 at 80iterations 0.1441800 2.384914 at 90iterations 8.4119953E-02 1.372728 at 100iterations 4.8935082E-02 0.8420563 at 110iterations 2.8537875E-02 0.4642696 at 120iterations 1.6654305E-02 0.2697449 at 130iterations 9.7158318E-03 0.1680832 at 140iterations 5.6585688E-03 9.9479675E-02 at 150iterations 3.3025481E-03 5.5008888E-02 at 160iterations 1.9236567E-03 3.1181335E-02 at 170iterations 1.1214473E-03 2.0414352E-02 at 180iterations finished qdiffx linear iterations at : 07:53:59 total time elapsed so far: 16.67000 # loops : 180 mean,max change (kT/e) : 1.1214473E-03 2.0414352E-02 energy calculations done at 16.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.85000 DelPhi exited at 07:54:00 16.852u 0.302s 0:17.46 98.2% 0+0k 0+0io 0pf+0w