Tue Oct 11 03:47:12 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 03:47:12 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6453484 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): -9.351000 37.19600 ymin,ymax (A): -27.47500 21.98800 zmin,zma (A): -9.925000 45.23900 x,y,z range (A): 46.54700 49.46300 55.16400 scale (grids/A): 0.6453484 object centre (A): 13.92250 -2.743501 17.65700 number of atom coordinates read : 2776 total number of charged atoms : 2670 net assigned charge : 1.588022 assigned positive charge : 430.2787 centred at (gu) : 89.18855 90.64577 91.81773 assigned negative charge : -428.6912 centred at (gu) : 88.94321 90.52528 91.81107 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7753 nv = 96 ne = 84 npr = 54841 no. pairs analyzed = 54841 no. exposed pairs = 3492 no. arc points = 23999 no. surface atoms = 1178 nbur = 1598 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4315 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3800000 number of dielectric boundary points 3812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2319 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9324 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3504047E-09 5.7359699E-09 midg,1,midg; midg,igrid,midg -1.3170618E-08 2.3615344E-08 1,midg,midg; igrid,midg,midg -4.1100382E-08 3.2199850E-08 gauss-seidel spectral radius is 0.9875727 estimated iterations to convergence 73 setup time was (sec) 0.6500000 now iterating at: 03:47:13 rms-change max change #iterations 0.1639270 23.62595 at 10iterations 1.6561527E-02 2.404198 at 20iterations 1.7002685E-03 0.2285252 at 30iterations 1.7274161E-04 2.2575378E-02 at 40iterations 1.8334715E-05 2.5177002E-03 at 50iterations finished qdiffx linear iterations at : 03:47:17 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.8334715E-05 2.5177002E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 03:47:17 4.167u 0.267s 0:04.80 92.0% 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 03:47:17 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.936045 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): -9.351000 37.19600 ymin,ymax (A): -27.47500 21.98800 zmin,zma (A): -9.925000 45.23900 x,y,z range (A): 46.54700 49.46300 55.16400 scale (grids/A): 1.936045 object centre (A): 13.92250 -2.743501 17.65700 number of atom coordinates read : 2776 total number of charged atoms : 2670 net assigned charge : 1.588022 assigned positive charge : 430.2787 centred at (gu) : 87.56496 91.93687 95.45246 assigned negative charge : -428.6912 centred at (gu) : 86.82925 91.57566 95.43300 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 83347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23999 grid for indexing accessible points = 1.400000 m= 30772 mr = 58369 m= 4860 mr = 22733 m= 354 mr = 2888 m= 5 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1607 time to turn everything in is 0.7300000 number of dielectric boundary points 35220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21027 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) : 0.6453484 object centre at (A) : 13.92250 -2.743501 17.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5342190E-02 1.0540009E-02 midg,1,midg; midg,igrid,midg -1.4988929E-02 8.0653960E-03 1,midg,midg; igrid,midg,midg -1.7736342E-02 4.7949512E-02 gauss-seidel spectral radius is 0.9986971 estimated iterations to convergence 219 setup time was (sec) 1.040000 now iterating at: 03:47:19 rms-change max change #iterations 4.668866 196.0091 at 10iterations 2.227654 80.25729 at 20iterations 1.063539 32.13474 at 30iterations 0.5069765 15.35780 at 40iterations 0.2415258 7.552849 at 50iterations 0.1148471 3.571648 at 60iterations 5.5104386E-02 1.707020 at 70iterations 2.6242236E-02 0.8385456 at 80iterations 1.2492962E-02 0.3872223 at 90iterations 5.9501827E-03 0.1745530 at 100iterations 2.8456398E-03 8.0348969E-02 at 110iterations 1.3581109E-03 3.8646698E-02 at 120iterations finished qdiffx linear iterations at : 03:47:27 total time elapsed so far: 9.570000 # loops : 120 mean,max change (kT/e) : 1.3581109E-03 3.8646698E-02 energy calculations done at 9.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 03:47:28 9.743u 0.327s 0:10.96 91.7% 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 Tue Oct 11 2011 at 03:47:28 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.904068 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): -9.351000 37.19600 ymin,ymax (A): -27.47500 21.98800 zmin,zma (A): -9.925000 45.23900 x,y,z range (A): 46.54700 49.46300 55.16400 scale (grids/A): 2.904068 object centre (A): 13.92250 -2.743501 17.65700 number of atom coordinates read : 2776 total number of charged atoms : 2670 net assigned charge : 1.588022 assigned positive charge : 430.2787 centred at (gu) : 86.34732 92.90509 98.17863 assigned negative charge : -428.6912 centred at (gu) : 85.24372 92.36332 98.14935 start vw surface at 0.1700000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 192593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23999 grid for indexing accessible points = 1.400000 m= 99708 mr = 141350 m= 36020 mr = 81767 m= 8664 mr = 28724 m= 1320 mr = 6257 m= 102 mr = 873 m= 0 mr = 49 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 5237 time to turn everything in is 1.930000 number of dielectric boundary points 79387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 21350 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) : 1.936045 object centre at (A) : 13.92250 -2.743501 17.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2798848 0.3929897 midg,1,midg; midg,igrid,midg -0.2018158 3.7460200E-02 1,midg,midg; igrid,midg,midg -8.5851572E-02 0.4778127 gauss-seidel spectral radius is 0.9992810 estimated iterations to convergence 294 setup time was (sec) 2.270000 now iterating at: 03:47:31 rms-change max change #iterations 10.93026 426.0334 at 10iterations 6.471100 163.9419 at 20iterations 3.822190 99.20583 at 30iterations 2.243622 48.68676 at 40iterations 1.317627 26.90163 at 50iterations 0.7686575 14.82168 at 60iterations 0.4474381 8.155987 at 70iterations 0.2610020 4.503296 at 80iterations 0.1518097 3.044260 at 90iterations 8.8376999E-02 1.711144 at 100iterations 5.1254217E-02 0.8458767 at 110iterations 2.9859841E-02 0.5151672 at 120iterations 1.7328741E-02 0.3240604 at 130iterations 1.0050706E-02 0.1877661 at 140iterations 5.8365408E-03 0.1046772 at 150iterations 3.3886833E-03 5.7779789E-02 at 160iterations 1.9659696E-03 3.5881996E-02 at 170iterations 1.1478184E-03 1.9033432E-02 at 180iterations finished qdiffx linear iterations at : 03:47:45 total time elapsed so far: 16.55000 # loops : 180 mean,max change (kT/e) : 1.1478184E-03 1.9033432E-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) 16.72000 DelPhi exited at 03:47:46 16.724u 0.317s 0:17.44 97.6% 0+0k 0+0io 0pf+0w