Tue Oct 11 03:15:50 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 03:15:50 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2141 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6776693 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): 34.68000 79.92700 ymin,ymax (A): 27.75800 76.31900 zmin,zma (A): 1.131000 53.66400 x,y,z range (A): 45.24700 48.56100 52.53300 scale (grids/A): 0.6776693 object centre (A): 57.30350 52.03850 27.39750 number of atom coordinates read : 2141 total number of charged atoms : 2042 net assigned charge : 3.000010 assigned positive charge : 322.1985 centred at (gu) : 89.54303 90.14040 88.68623 assigned negative charge : -319.1989 centred at (gu) : 89.47920 90.13795 88.49863 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6808 nv = 96 ne = 84 npr = 42954 no. pairs analyzed = 42954 no. exposed pairs = 2819 no. arc points = 20078 no. surface atoms = 937 nbur = 1204 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3697 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1829 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7818 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6743057E-08 4.5475019E-08 midg,1,midg; midg,igrid,midg 1.2013129E-08 1.3964351E-08 1,midg,midg; igrid,midg,midg -3.6439998E-09 2.6412245E-08 gauss-seidel spectral radius is 0.9886754 estimated iterations to convergence 77 setup time was (sec) 0.5700000 now iterating at: 03:15:51 rms-change max change #iterations 0.1689962 27.66604 at 10iterations 1.9021325E-02 2.871033 at 20iterations 2.1773081E-03 0.2888908 at 30iterations 3.0292326E-04 4.9587250E-02 at 40iterations 6.3906737E-05 1.1596680E-02 at 50iterations finished qdiffx linear iterations at : 03:15:56 total time elapsed so far: 4.880000 # loops : 50 mean,max change (kT/e) : 6.3906737E-05 1.1596680E-02 energy calculations done at 4.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.060000 DelPhi exited at 03:15:57 5.063u 0.425s 0:06.19 88.5% 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 03:15:57 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2141 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.033008 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): 34.68000 79.92700 ymin,ymax (A): 27.75800 76.31900 zmin,zma (A): 1.131000 53.66400 x,y,z range (A): 45.24700 48.56100 52.53300 scale (grids/A): 2.033008 object centre (A): 57.30350 52.03850 27.39750 number of atom coordinates read : 2141 total number of charged atoms : 2042 net assigned charge : 3.000010 assigned positive charge : 322.1985 centred at (gu) : 88.62853 90.42100 86.05824 assigned negative charge : -319.1989 centred at (gu) : 88.43755 90.41379 85.49606 start vw surface at 0.1000000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20078 grid for indexing accessible points = 1.400000 m= 27027 mr = 49877 m= 5123 mr = 19903 m= 422 mr = 3309 m= 10 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 229 time to turn everything in is 0.6100000 number of dielectric boundary points 32088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 16195 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) : 0.6776693 object centre at (A) : 57.30350 52.03850 27.39750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8817335E-02 5.7660151E-02 midg,1,midg; midg,igrid,midg -2.8001549E-02 9.7830249E-03 1,midg,midg; igrid,midg,midg -1.1997840E-02 1.4398026E-02 gauss-seidel spectral radius is 0.9987584 estimated iterations to convergence 225 setup time was (sec) 0.9900000 now iterating at: 03:15:58 rms-change max change #iterations 4.325297 189.6515 at 10iterations 2.095337 80.43434 at 20iterations 1.014866 34.21358 at 30iterations 0.4930437 15.39709 at 40iterations 0.2397174 8.259131 at 50iterations 0.1159651 3.561152 at 60iterations 5.6289755E-02 1.758133 at 70iterations 2.7253237E-02 0.8740253 at 80iterations 1.3230513E-02 0.4200664 at 90iterations 6.4455662E-03 0.1945534 at 100iterations 3.1369254E-03 9.9433899E-02 at 110iterations 1.5417074E-03 4.8466682E-02 at 120iterations finished qdiffx linear iterations at : 03:16:10 total time elapsed so far: 12.17000 # loops : 120 mean,max change (kT/e) : 1.5417074E-03 4.8466682E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 03:16:10 12.331u 0.530s 0:13.29 96.7% 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 03:16:10 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2141 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.049512 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): 34.68000 79.92700 ymin,ymax (A): 27.75800 76.31900 zmin,zma (A): 1.131000 53.66400 x,y,z range (A): 45.24700 48.56100 52.53300 scale (grids/A): 3.049512 object centre (A): 57.30350 52.03850 27.39750 number of atom coordinates read : 2141 total number of charged atoms : 2042 net assigned charge : 3.000010 assigned positive charge : 322.1985 centred at (gu) : 87.94270 90.63140 84.08721 assigned negative charge : -319.1989 centred at (gu) : 87.65637 90.62074 83.24409 start vw surface at 0.1000000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 168109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20078 grid for indexing accessible points = 1.400000 m= 84589 mr = 120917 m= 34005 mr = 68703 m= 9542 mr = 27518 m= 1688 mr = 7267 m= 160 mr = 1114 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 1.640000 number of dielectric boundary points 72501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 16336 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) : 2.033008 object centre at (A) : 57.30350 52.03850 27.39750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4629625 0.5482175 midg,1,midg; midg,igrid,midg -0.3178539 0.1562537 1,midg,midg; igrid,midg,midg -0.1403261 9.8832160E-02 gauss-seidel spectral radius is 0.9992934 estimated iterations to convergence 297 setup time was (sec) 2.030000 now iterating at: 03:16:13 rms-change max change #iterations 9.946474 516.3862 at 10iterations 5.855956 141.9215 at 20iterations 3.441706 70.37858 at 30iterations 2.016815 47.85104 at 40iterations 1.182209 22.40892 at 50iterations 0.6910135 13.12644 at 60iterations 0.4033222 7.677427 at 70iterations 0.2349429 4.114857 at 80iterations 0.1369511 2.482575 at 90iterations 7.9785347E-02 1.597179 at 100iterations 4.6643954E-02 0.8237000 at 110iterations 2.7120093E-02 0.4756851 at 120iterations 1.5794015E-02 0.2807617 at 130iterations 9.2201484E-03 0.1642017 at 140iterations 5.3727301E-03 8.9408875E-02 at 150iterations 3.1465623E-03 5.6930542E-02 at 160iterations 1.8495598E-03 3.2462597E-02 at 170iterations 1.0984004E-03 2.0406723E-02 at 180iterations finished qdiffx linear iterations at : 03:16:31 total time elapsed so far: 20.40000 # loops : 180 mean,max change (kT/e) : 1.0984004E-03 2.0406723E-02 energy calculations done at 20.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.56000 DelPhi exited at 03:16:32 20.561u 0.565s 0:21.51 98.1% 0+0k 0+0io 0pf+0w