Sat Oct 8 17:29:03 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 17:29:03 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3462 !!! WARNING: ILE 375 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5544912 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): 36.54000 93.20300 ymin,ymax (A): 16.38500 80.58801 zmin,zma (A): -22.86400 25.36100 x,y,z range (A): 56.66300 64.20300 48.22500 scale (grids/A): 0.5544912 object centre (A): 64.87151 48.48650 1.248500 number of atom coordinates read : 3462 total number of charged atoms : 3316 net assigned charge : -5.271986 assigned positive charge : 524.7831 centred at (gu) : 90.44212 89.87884 89.75598 assigned negative charge : -530.0569 centred at (gu) : 90.47163 89.86405 89.73283 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6890 nv = 96 ne = 84 npr = 70346 no. pairs analyzed = 70346 no. exposed pairs = 4221 no. arc points = 28837 no. surface atoms = 1432 nbur = 2030 mkacc time = 0.1500000 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 = 1.568000 m= 278 mr = 3729 m= 0 mr = 22 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2951 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8968 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.4810069E-10 -1.9246899E-10 midg,1,midg; midg,igrid,midg -6.3232453E-10 -2.8539129E-10 1,midg,midg; igrid,midg,midg -1.2269095E-10 -8.6246182E-10 gauss-seidel spectral radius is 0.9832594 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 17:29:04 rms-change max change #iterations 8.8564120E-02 16.08001 at 10iterations 6.1058258E-03 1.017717 at 20iterations 4.5538743E-04 6.6837311E-02 at 30iterations 5.3653588E-05 1.1960030E-02 at 40iterations 1.1204778E-05 2.9907227E-03 at 50iterations finished qdiffx linear iterations at : 17:29:06 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.1204778E-05 2.9907227E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 17:29:07 3.503u 0.226s 0:04.01 92.7% 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 17:29:07 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3462 !!! WARNING: ILE 375 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.663474 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): 36.54000 93.20300 ymin,ymax (A): 16.38500 80.58801 zmin,zma (A): -22.86400 25.36100 x,y,z range (A): 56.66300 64.20300 48.22500 scale (grids/A): 1.663474 object centre (A): 64.87151 48.48650 1.248500 number of atom coordinates read : 3462 total number of charged atoms : 3316 net assigned charge : -5.271986 assigned positive charge : 524.7831 centred at (gu) : 91.32497 89.63571 89.26723 assigned negative charge : -530.0569 centred at (gu) : 91.41459 89.59180 89.19809 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28837 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25062 mr = 53162 m= 2953 mr = 17890 m= 87 mr = 1686 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 726 time to turn everything in is 0.5400000 number of dielectric boundary points 31593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 25504 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) : 0.5544912 object centre at (A) : 64.87151 48.48650 1.248500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6518571E-03 -5.0929110E-03 midg,1,midg; midg,igrid,midg 6.5579317E-03 1.6399505E-02 1,midg,midg; igrid,midg,midg -1.4968095E-02 -7.6498808E-03 gauss-seidel spectral radius is 0.9982962 estimated iterations to convergence 192 setup time was (sec) 0.8500000 now iterating at: 17:29:08 rms-change max change #iterations 3.812267 196.8886 at 10iterations 1.626092 63.42780 at 20iterations 0.6967915 25.77255 at 30iterations 0.2988523 9.984642 at 40iterations 0.1282288 4.602605 at 50iterations 5.5040047E-02 1.863618 at 60iterations 2.3580067E-02 0.8090019 at 70iterations 1.0151669E-02 0.3254766 at 80iterations 4.3708058E-03 0.1337700 at 90iterations 1.8755283E-03 6.0021400E-02 at 100iterations 8.0852932E-04 2.6579857E-02 at 110iterations 3.5058853E-04 1.2039900E-02 at 120iterations finished qdiffx linear iterations at : 17:29:15 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 3.5058853E-04 1.2039900E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 17:29:15 7.849u 0.272s 0:08.39 96.6% 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 17:29:15 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3462 !!! WARNING: ILE 375 has a net charge of -0.2720 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: 2.495210 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): 36.54000 93.20300 ymin,ymax (A): 16.38500 80.58801 zmin,zma (A): -22.86400 25.36100 x,y,z range (A): 56.66300 64.20300 48.22500 scale (grids/A): 2.495210 object centre (A): 64.87151 48.48650 1.248500 number of atom coordinates read : 3462 total number of charged atoms : 3316 net assigned charge : -5.271986 assigned positive charge : 524.7831 centred at (gu) : 91.98729 89.45338 88.90033 assigned negative charge : -530.0569 centred at (gu) : 92.12182 89.38757 88.79705 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 177168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28837 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 85320 mr = 129798 m= 26037 mr = 68908 m= 4918 mr = 20205 m= 495 mr = 3548 m= 10 mr = 297 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 2503 time to turn everything in is 1.320000 number of dielectric boundary points 71192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 26497 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) : 1.663474 object centre at (A) : 64.87151 48.48650 1.248500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1721256E-02 -5.4330140E-02 midg,1,midg; midg,igrid,midg 0.2994270 0.4467274 1,midg,midg; igrid,midg,midg -0.2633513 -6.1829794E-02 gauss-seidel spectral radius is 0.9991794 estimated iterations to convergence 276 setup time was (sec) 1.640000 now iterating at: 17:29:17 rms-change max change #iterations 9.738180 355.3388 at 10iterations 5.529506 138.7905 at 20iterations 3.134003 69.67719 at 30iterations 1.765066 37.76042 at 40iterations 0.9935808 20.13342 at 50iterations 0.5559874 10.65991 at 60iterations 0.3121364 6.512741 at 70iterations 0.1742211 3.218678 at 80iterations 9.7552568E-02 1.882290 at 90iterations 5.4548137E-02 1.069177 at 100iterations 3.0438617E-02 0.5718384 at 110iterations 1.6967857E-02 0.3274527 at 120iterations 9.4852531E-03 0.1847894 at 130iterations 5.2945954E-03 9.4635487E-02 at 140iterations 2.9568844E-03 6.3705444E-02 at 150iterations 1.6533136E-03 3.5957336E-02 at 160iterations 9.2552166E-04 1.8342018E-02 at 170iterations 5.1862095E-04 1.0680199E-02 at 180iterations finished qdiffx linear iterations at : 17:29:28 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 5.1862095E-04 1.0680199E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 17:29:29 12.984u 0.278s 0:13.54 97.8% 0+0k 0+0io 0pf+0w