Tue Oct 11 03:45:07 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 03:45:07 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: GLN 307 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6000033 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): -12.08400 36.80200 ymin,ymax (A): 3.484000 51.94900 zmin,zma (A): -13.63700 45.69600 x,y,z range (A): 48.88600 48.46500 59.33300 scale (grids/A): 0.6000033 object centre (A): 12.35900 27.71650 16.02950 number of atom coordinates read : 2940 total number of charged atoms : 2789 net assigned charge : 3.742028 assigned positive charge : 451.9556 centred at (gu) : 90.14677 89.90456 92.14532 assigned negative charge : -448.2141 centred at (gu) : 89.93679 89.73593 92.07987 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6919 nv = 96 ne = 84 npr = 59745 no. pairs analyzed = 59745 no. exposed pairs = 3516 no. arc points = 24506 no. surface atoms = 1188 nbur = 1752 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3871 m= 4 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4200000 number of dielectric boundary points 3356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2469 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 8668 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2644657E-10 6.9823156E-09 midg,1,midg; midg,igrid,midg -5.8012013E-09 8.2935250E-09 1,midg,midg; igrid,midg,midg -7.2323090E-09 1.0484168E-08 gauss-seidel spectral radius is 0.9856460 estimated iterations to convergence 68 setup time was (sec) 0.7400000 now iterating at: 03:45:08 rms-change max change #iterations 0.1219680 19.30997 at 10iterations 1.0709992E-02 1.867120 at 20iterations 1.4588404E-03 0.2364063 at 30iterations 5.1398476E-04 9.9527359E-02 at 40iterations 2.3126979E-04 4.4481277E-02 at 50iterations finished qdiffx linear iterations at : 03:45:11 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 2.3126979E-04 4.4481277E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 03:45:12 4.403u 0.263s 0:05.11 91.1% 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 Tue Oct 11 2011 at 03:45:12 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: GLN 307 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.800010 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): -12.08400 36.80200 ymin,ymax (A): 3.484000 51.94900 zmin,zma (A): -13.63700 45.69600 x,y,z range (A): 48.88600 48.46500 59.33300 scale (grids/A): 1.800010 object centre (A): 12.35900 27.71650 16.02950 number of atom coordinates read : 2940 total number of charged atoms : 2789 net assigned charge : 3.742028 assigned positive charge : 451.9556 centred at (gu) : 90.43961 89.71313 96.43546 assigned negative charge : -448.2141 centred at (gu) : 89.80990 89.20741 96.23921 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 75665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24506 grid for indexing accessible points = 1.400000 m= 26032 mr = 53306 m= 3469 mr = 19068 m= 120 mr = 1968 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.7300000 number of dielectric boundary points 30923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21745 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) : 0.6000033 object centre at (A) : 12.35900 27.71650 16.02950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6159562E-02 1.7473898E-03 midg,1,midg; midg,igrid,midg -6.4889742E-03 2.0737667E-02 1,midg,midg; igrid,midg,midg -4.5654359E-03 3.7575074E-02 gauss-seidel spectral radius is 0.9985066 estimated iterations to convergence 205 setup time was (sec) 1.120000 now iterating at: 03:45:13 rms-change max change #iterations 4.162987 177.8214 at 10iterations 1.880292 66.21373 at 20iterations 0.8503200 28.26005 at 30iterations 0.3857229 11.54827 at 40iterations 0.1749216 5.880585 at 50iterations 7.9675190E-02 2.693752 at 60iterations 3.6070812E-02 1.080594 at 70iterations 1.6478376E-02 0.6102180 at 80iterations 7.6108654E-03 0.2560253 at 90iterations 3.6321785E-03 0.1216240 at 100iterations 1.8460555E-03 6.6577196E-02 at 110iterations 1.0506919E-03 4.3018341E-02 at 120iterations finished qdiffx linear iterations at : 03:45:23 total time elapsed so far: 10.44000 # loops : 120 mean,max change (kT/e) : 1.0506919E-03 4.3018341E-02 energy calculations done at 10.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 03:45:23 10.669u 0.269s 0:11.29 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 03:45:23 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: GLN 307 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: 2.700015 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): -12.08400 36.80200 ymin,ymax (A): 3.484000 51.94900 zmin,zma (A): -13.63700 45.69600 x,y,z range (A): 48.88600 48.46500 59.33300 scale (grids/A): 2.700015 object centre (A): 12.35900 27.71650 16.02950 number of atom coordinates read : 2940 total number of charged atoms : 2789 net assigned charge : 3.742028 assigned positive charge : 451.9556 centred at (gu) : 90.65928 89.56966 99.65294 assigned negative charge : -448.2141 centred at (gu) : 89.71479 88.81104 99.35885 start vw surface at 0.1900000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 175011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24506 grid for indexing accessible points = 1.400000 m= 87181 mr = 128974 m= 28794 mr = 71390 m= 5890 mr = 22805 m= 630 mr = 4226 m= 22 mr = 323 m= 0 mr = 1 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 553 time to turn everything in is 1.750000 number of dielectric boundary points 69809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 22308 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) : 1.800010 object centre at (A) : 12.35900 27.71650 16.02950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.245576 0.1854649 midg,1,midg; midg,igrid,midg -8.3618492E-02 0.2427355 1,midg,midg; igrid,midg,midg -5.1723752E-02 0.3717545 gauss-seidel spectral radius is 0.9992257 estimated iterations to convergence 284 setup time was (sec) 2.140000 now iterating at: 03:45:26 rms-change max change #iterations 10.07075 298.4340 at 10iterations 5.877398 164.2272 at 20iterations 3.402777 91.47574 at 30iterations 1.963531 39.34113 at 40iterations 1.128305 23.78637 at 50iterations 0.6480134 14.01481 at 60iterations 0.3711494 8.280380 at 70iterations 0.2121740 4.152405 at 80iterations 0.1210553 2.446363 at 90iterations 6.9103360E-02 1.466311 at 100iterations 3.9548554E-02 0.7733006 at 110iterations 2.2504136E-02 0.4697952 at 120iterations 1.2924148E-02 0.2822561 at 130iterations 7.4578454E-03 0.1672668 at 140iterations 4.3395790E-03 8.3130360E-02 at 150iterations 2.5919804E-03 5.2997589E-02 at 160iterations 1.6106321E-03 3.6327362E-02 at 170iterations 1.0672609E-03 2.3069382E-02 at 180iterations finished qdiffx linear iterations at : 03:45:39 total time elapsed so far: 15.67000 # loops : 180 mean,max change (kT/e) : 1.0672609E-03 2.3069382E-02 energy calculations done at 15.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 03:45:40 15.908u 0.301s 0:16.58 97.7% 0+0k 0+0io 0pf+0w