Sat Oct 8 20:45:21 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 20:45:21 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 357 has a net charge of 1.4000 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: 0.6270476 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): -11.20700 38.78300 ymin,ymax (A): -21.90800 24.67700 zmin,zma (A): -12.11200 44.66200 x,y,z range (A): 49.99000 46.58500 56.77400 scale (grids/A): 0.6270476 object centre (A): 13.78800 1.384501 16.27500 number of atom coordinates read : 2584 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.6440 centred at (gu) : 88.74844 89.25512 89.72681 assigned negative charge : -388.7386 centred at (gu) : 88.64972 89.30338 89.60049 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6598 nv = 96 ne = 84 npr = 53868 no. pairs analyzed = 53868 no. exposed pairs = 3095 no. arc points = 21864 no. surface atoms = 1034 nbur = 1550 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3631 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.2900000 number of dielectric boundary points 3236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2121 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8171 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8280679E-09 1.3317480E-08 midg,1,midg; midg,igrid,midg 9.3017176E-09 8.0586281E-11 1,midg,midg; igrid,midg,midg -5.5196998E-09 9.1091650E-09 gauss-seidel spectral radius is 0.9868199 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 20:45:22 rms-change max change #iterations 0.1321986 17.50163 at 10iterations 1.2835915E-02 1.832275 at 20iterations 1.4431699E-03 0.2486029 at 30iterations 3.1045871E-04 6.1243057E-02 at 40iterations 9.8456592E-05 2.0685196E-02 at 50iterations finished qdiffx linear iterations at : 20:45:25 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 9.8456592E-05 2.0685196E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 20:45:25 3.296u 0.183s 0:03.74 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 20:45:25 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 357 has a net charge of 1.4000 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: 1.881143 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): -11.20700 38.78300 ymin,ymax (A): -21.90800 24.67700 zmin,zma (A): -12.11200 44.66200 x,y,z range (A): 49.99000 46.58500 56.77400 scale (grids/A): 1.881143 object centre (A): 13.78800 1.384501 16.27500 number of atom coordinates read : 2584 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.6440 centred at (gu) : 86.24487 87.76527 89.17994 assigned negative charge : -388.7386 centred at (gu) : 85.94884 87.91006 88.80145 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71561 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21864 grid for indexing accessible points = 1.400000 m= 24777 mr = 49922 m= 3703 mr = 18106 m= 179 mr = 2284 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2608 time to turn everything in is 0.5200000 number of dielectric boundary points 29862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19270 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) : 0.6270476 object centre at (A) : 13.78800 1.384501 16.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4910898E-02 2.2003541E-02 midg,1,midg; midg,igrid,midg 1.2896372E-02 1.1414052E-03 1,midg,midg; igrid,midg,midg -5.9127975E-03 3.7128493E-02 gauss-seidel spectral radius is 0.9985957 estimated iterations to convergence 212 setup time was (sec) 0.8200000 now iterating at: 20:45:26 rms-change max change #iterations 4.131125 169.0188 at 10iterations 1.915872 75.87697 at 20iterations 0.8845709 27.66026 at 30iterations 0.4100999 14.45659 at 40iterations 0.1902679 6.734576 at 50iterations 8.8127255E-02 2.714103 at 60iterations 4.0908620E-02 1.604485 at 70iterations 1.9065855E-02 0.6148281 at 80iterations 8.8745011E-03 0.2770896 at 90iterations 4.1639954E-03 0.1516867 at 100iterations 1.9879406E-03 6.1641693E-02 at 110iterations 9.8449166E-04 3.6172867E-02 at 120iterations finished qdiffx linear iterations at : 20:45:33 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 9.8449166E-04 3.6172867E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 20:45:33 7.652u 0.246s 0:08.21 96.1% 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 20:45:33 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 357 has a net charge of 1.4000 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: 2.821714 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): -11.20700 38.78300 ymin,ymax (A): -21.90800 24.67700 zmin,zma (A): -12.11200 44.66200 x,y,z range (A): 49.99000 46.58500 56.77400 scale (grids/A): 2.821714 object centre (A): 13.78800 1.384501 16.27500 number of atom coordinates read : 2584 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.6440 centred at (gu) : 84.36716 86.64777 88.76972 assigned negative charge : -388.7386 centred at (gu) : 83.92316 86.86500 88.20204 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 165880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21864 grid for indexing accessible points = 1.400000 m= 82208 mr = 121101 m= 27926 mr = 67232 m= 6495 mr = 22119 m= 849 mr = 4933 m= 32 mr = 527 m= 0 mr = 13 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 8795 time to turn everything in is 1.270000 number of dielectric boundary points 67465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 19599 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) : 1.881143 object centre at (A) : 13.78800 1.384501 16.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9577132E-02 0.2349695 midg,1,midg; midg,igrid,midg 0.1594792 -6.5366477E-03 1,midg,midg; igrid,midg,midg -6.3515097E-02 0.4678212 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.550000 now iterating at: 20:45:35 rms-change max change #iterations 9.696321 278.9048 at 10iterations 5.604573 130.3652 at 20iterations 3.213696 67.67422 at 30iterations 1.845645 39.39293 at 40iterations 1.057225 21.22406 at 50iterations 0.6054091 11.52590 at 60iterations 0.3471029 6.305006 at 70iterations 0.1983960 4.103806 at 80iterations 0.1134059 2.055543 at 90iterations 6.4865395E-02 1.242218 at 100iterations 3.7061140E-02 0.6431222 at 110iterations 2.1185277E-02 0.4259276 at 120iterations 1.2093650E-02 0.2349701 at 130iterations 6.9534178E-03 0.1286087 at 140iterations 3.9810152E-03 8.7516785E-02 at 150iterations 2.2930454E-03 4.2276382E-02 at 160iterations 1.3332833E-03 2.8118134E-02 at 170iterations 7.9138239E-04 1.6201019E-02 at 180iterations finished qdiffx linear iterations at : 20:45:45 total time elapsed so far: 11.09000 # loops : 180 mean,max change (kT/e) : 7.9138239E-04 1.6201019E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 20:45:45 11.281u 0.157s 0:11.72 97.5% 0+0k 0+0io 0pf+0w