Wed Feb 15 08:56:14 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:14 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: FMN 398 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6677420 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 0.6677420 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2545 net assigned charge : 2.500011 assigned positive charge : 408.8235 centred at (gu) : 90.85991 90.33403 90.34605 assigned negative charge : -406.3244 centred at (gu) : 90.69237 90.54635 90.39133 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7974 nv = 96 ne = 84 npr = 56759 no. pairs analyzed = 56759 no. exposed pairs = 3246 no. arc points = 22269 no. surface atoms = 1089 nbur = 1591 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4527 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.3400000 number of dielectric boundary points 3825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2150 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9431 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7796340E-08 -4.0204227E-09 midg,1,midg; midg,igrid,midg 5.6032164E-08 -5.0407341E-08 1,midg,midg; igrid,midg,midg -2.9337757E-08 5.8932912E-08 gauss-seidel spectral radius is 0.9883792 estimated iterations to convergence 76 setup time was (sec) 0.5900000 now iterating at: 08:56:15 rms-change max change #iterations 0.1831875 29.46806 at 10iterations 2.0896161E-02 3.065392 at 20iterations 3.1005125E-03 0.5148010 at 30iterations 8.4178976E-04 0.1789093 at 40iterations 2.9886694E-04 6.5177917E-02 at 50iterations finished qdiffx linear iterations at : 08:56:18 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 2.9886694E-04 6.5177917E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 08:56:19 3.736u 0.203s 0:04.37 89.9% 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 Wed Feb 15 2012 at 08:56:19 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: FMN 398 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.003226 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 2.003226 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2545 net assigned charge : 2.500011 assigned positive charge : 408.8235 centred at (gu) : 92.57921 91.00117 91.03729 assigned negative charge : -406.3244 centred at (gu) : 92.07698 91.63872 91.17348 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 86049 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22269 grid for indexing accessible points = 1.400000 m= 32158 mr = 60984 m= 5408 mr = 24171 m= 361 mr = 3486 m= 6 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1702 time to turn everything in is 0.6600000 number of dielectric boundary points 35183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20135 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) : 0.6677420 object centre at (A) : 43.97850 41.31400 6.246000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4958141E-02 -3.4187164E-02 midg,1,midg; midg,igrid,midg 6.0225770E-02 -5.4264840E-02 1,midg,midg; igrid,midg,midg -2.2932930E-02 4.9828514E-02 gauss-seidel spectral radius is 0.9987676 estimated iterations to convergence 226 setup time was (sec) 0.9600000 now iterating at: 08:56:20 rms-change max change #iterations 4.832949 191.0822 at 10iterations 2.350068 84.35423 at 20iterations 1.145191 38.73798 at 30iterations 0.5576303 16.65663 at 40iterations 0.2712438 8.270447 at 50iterations 0.1322801 3.909793 at 60iterations 6.4611383E-02 1.864875 at 70iterations 3.1644676E-02 0.8927765 at 80iterations 1.5694903E-02 0.4611053 at 90iterations 7.9251863E-03 0.3045807 at 100iterations 4.1458406E-03 0.1605692 at 110iterations 2.2968764E-03 8.5815430E-02 at 120iterations finished qdiffx linear iterations at : 08:56:28 total time elapsed so far: 8.230000 # loops : 120 mean,max change (kT/e) : 2.2968764E-03 8.5815430E-02 energy calculations done at 8.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 08:56:28 8.434u 0.308s 0:09.30 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 Wed Feb 15 2012 at 08:56:28 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: FMN 398 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.004839 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 3.004839 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2545 net assigned charge : 2.500011 assigned positive charge : 408.8235 centred at (gu) : 93.86861 91.50153 91.55583 assigned negative charge : -406.3244 centred at (gu) : 93.11552 92.45807 91.76019 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 198702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22269 grid for indexing accessible points = 1.400000 m= 103257 mr = 147448 m= 38934 mr = 85432 m= 9962 mr = 31674 m= 1603 mr = 7573 m= 106 mr = 1134 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 5733 time to turn everything in is 1.680000 number of dielectric boundary points 79258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 20359 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) : 2.003226 object centre at (A) : 43.97850 41.31400 6.246000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1828474 -0.3911687 midg,1,midg; midg,igrid,midg 0.8438930 -0.6802825 1,midg,midg; igrid,midg,midg -0.2458606 0.3904910 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 2.010000 now iterating at: 08:56:31 rms-change max change #iterations 11.01848 468.8723 at 10iterations 6.487497 132.2228 at 20iterations 3.818257 75.69125 at 30iterations 2.237374 39.32838 at 40iterations 1.311183 23.25820 at 50iterations 0.7654278 13.88532 at 60iterations 0.4476733 7.745216 at 70iterations 0.2614935 5.747959 at 80iterations 0.1525436 2.923981 at 90iterations 8.8797569E-02 1.512829 at 100iterations 5.1958717E-02 0.8417101 at 110iterations 3.0373005E-02 0.5263252 at 120iterations 1.7859951E-02 0.3354111 at 130iterations 1.0556030E-02 0.2089729 at 140iterations 6.3729226E-03 0.1365967 at 150iterations 3.9418917E-03 8.7913513E-02 at 160iterations 2.5667378E-03 6.0729980E-02 at 170iterations 1.7753885E-03 4.2343140E-02 at 180iterations finished qdiffx linear iterations at : 08:56:42 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 1.7753885E-03 4.2343140E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 08:56:43 13.425u 0.324s 0:14.42 95.2% 0+0k 0+0io 0pf+0w