Sun Oct 9 06:19:11 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 Sun Oct 9 2011 at 06:19:11 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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: 0.6691855 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): 1.995000 44.34700 ymin,ymax (A): -9.072001 37.87800 zmin,zma (A): -24.49100 28.70800 x,y,z range (A): 42.35200 46.95000 53.19900 scale (grids/A): 0.6691855 object centre (A): 23.17100 14.40300 2.108500 number of atom coordinates read : 1990 total number of charged atoms : 1847 net assigned charge : -1.593986 assigned positive charge : 300.6720 centred at (gu) : 90.12780 89.28869 88.49725 assigned negative charge : -302.2661 centred at (gu) : 89.97904 89.12788 88.45118 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6078 nv = 96 ne = 84 npr = 41521 no. pairs analyzed = 41521 no. exposed pairs = 2546 no. arc points = 17895 no. surface atoms = 858 nbur = 1132 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3304 m= 0 mr = 66 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2600000 number of dielectric boundary points 3079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6986 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8737506E-08 2.9567149E-09 midg,1,midg; midg,igrid,midg -4.2293689E-08 2.2281318E-08 1,midg,midg; igrid,midg,midg -3.3138470E-08 2.4278121E-08 gauss-seidel spectral radius is 0.9883712 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 06:19:11 rms-change max change #iterations 0.1550394 25.51748 at 10iterations 1.7182110E-02 2.823521 at 20iterations 1.8538299E-03 0.2539773 at 30iterations 2.0565392E-04 2.9891968E-02 at 40iterations 2.2346270E-05 4.0130615E-03 at 50iterations finished qdiffx linear iterations at : 06:19:14 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.2346270E-05 4.0130615E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:19:15 3.336u 0.184s 0:03.79 92.6% 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 Sun Oct 9 2011 at 06:19:15 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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: 2.007556 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): 1.995000 44.34700 ymin,ymax (A): -9.072001 37.87800 zmin,zma (A): -24.49100 28.70800 x,y,z range (A): 42.35200 46.95000 53.19900 scale (grids/A): 2.007556 object centre (A): 23.17100 14.40300 2.108500 number of atom coordinates read : 1990 total number of charged atoms : 1847 net assigned charge : -1.593986 assigned positive charge : 300.6720 centred at (gu) : 90.38339 87.86600 85.49155 assigned negative charge : -302.2661 centred at (gu) : 89.93727 87.38388 85.35361 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17895 grid for indexing accessible points = 1.400000 m= 24418 mr = 44095 m= 4473 mr = 18363 m= 368 mr = 3055 m= 11 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1987 time to turn everything in is 0.4800000 number of dielectric boundary points 28236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14591 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) : 0.6691855 object centre at (A) : 23.17100 14.40300 2.108500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1194733E-02 2.7405195E-02 midg,1,midg; midg,igrid,midg -3.3154693E-02 1.2861110E-02 1,midg,midg; igrid,midg,midg -2.9927773E-02 1.5627764E-02 gauss-seidel spectral radius is 0.9987078 estimated iterations to convergence 220 setup time was (sec) 0.7700000 now iterating at: 06:19:16 rms-change max change #iterations 4.175142 256.0542 at 10iterations 1.980260 86.60989 at 20iterations 0.9483681 29.75296 at 30iterations 0.4530525 16.37472 at 40iterations 0.2156368 6.942506 at 50iterations 0.1029595 3.367731 at 60iterations 4.9236372E-02 1.692131 at 70iterations 2.3497734E-02 0.7923155 at 80iterations 1.1240419E-02 0.3637285 at 90iterations 5.3808303E-03 0.1919818 at 100iterations 2.5717225E-03 8.5772514E-02 at 110iterations 1.2234707E-03 4.4548988E-02 at 120iterations finished qdiffx linear iterations at : 06:19:22 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.2234707E-03 4.4548988E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 06:19:23 7.468u 0.232s 0:07.96 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 Sun Oct 9 2011 at 06:19:23 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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: 3.011335 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): 1.995000 44.34700 ymin,ymax (A): -9.072001 37.87800 zmin,zma (A): -24.49100 28.70800 x,y,z range (A): 42.35200 46.95000 53.19900 scale (grids/A): 3.011335 object centre (A): 23.17100 14.40300 2.108500 number of atom coordinates read : 1990 total number of charged atoms : 1847 net assigned charge : -1.593986 assigned positive charge : 300.6720 centred at (gu) : 90.57497 86.79910 83.23745 assigned negative charge : -302.2661 centred at (gu) : 89.90587 86.07590 83.03043 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 148769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17895 grid for indexing accessible points = 1.400000 m= 77333 mr = 106106 m= 30092 mr = 63959 m= 8406 mr = 24732 m= 1563 mr = 6667 m= 153 mr = 1128 m= 6 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 6867 time to turn everything in is 1.200000 number of dielectric boundary points 63653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14776 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) : 2.007556 object centre at (A) : 23.17100 14.40300 2.108500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5046708 0.8734702 midg,1,midg; midg,igrid,midg -0.3062925 0.1566611 1,midg,midg; igrid,midg,midg -0.2879467 0.1123284 gauss-seidel spectral radius is 0.9992625 estimated iterations to convergence 291 setup time was (sec) 1.520000 now iterating at: 06:19:24 rms-change max change #iterations 9.479273 410.4916 at 10iterations 5.471374 132.5530 at 20iterations 3.152416 72.24545 at 30iterations 1.817480 38.30022 at 40iterations 1.048405 21.25684 at 50iterations 0.6023365 12.44308 at 60iterations 0.3467534 6.989807 at 70iterations 0.1986884 4.233236 at 80iterations 0.1143086 2.147140 at 90iterations 6.5482222E-02 1.306076 at 100iterations 3.7566785E-02 0.7350764 at 110iterations 2.1599356E-02 0.4513168 at 120iterations 1.2396945E-02 0.2352905 at 130iterations 7.1257576E-03 0.1375618 at 140iterations 4.0820548E-03 9.3017578E-02 at 150iterations 2.3517061E-03 4.6110630E-02 at 160iterations 1.3508780E-03 2.6962280E-02 at 170iterations 7.7327323E-04 1.4831543E-02 at 180iterations finished qdiffx linear iterations at : 06:19:35 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 7.7327323E-04 1.4831543E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 06:19:35 12.046u 0.237s 0:12.54 97.8% 0+0k 0+0io 0pf+0w