Tue Oct 11 07:17:51 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 07:17:51 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5837118 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): 0.4169999 49.96400 ymin,ymax (A): -8.383000 52.60600 zmin,zma (A): 1.254000 60.70900 x,y,z range (A): 49.54700 60.98900 59.45500 scale (grids/A): 0.5837118 object centre (A): 25.19050 22.11150 30.98150 number of atom coordinates read : 3424 total number of charged atoms : 3273 net assigned charge : 7.8380108E-06 assigned positive charge : 515.9973 centred at (gu) : 89.59674 89.18731 90.51739 assigned negative charge : -515.9987 centred at (gu) : 89.50070 89.16901 90.51928 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7525 nv = 96 ne = 84 npr = 71165 no. pairs analyzed = 71165 no. exposed pairs = 4119 no. arc points = 27679 no. surface atoms = 1402 nbur = 2022 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 317 mr = 4232 m= 0 mr = 14 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3900000 number of dielectric boundary points 3596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2862 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4968940E-11 -4.0432522E-11 midg,1,midg; midg,igrid,midg -6.1963784E-10 4.5073587E-10 1,midg,midg; igrid,midg,midg -3.0650100E-09 2.5084490E-09 gauss-seidel spectral radius is 0.9848781 estimated iterations to convergence 67 setup time was (sec) 0.6500000 now iterating at: 07:17:52 rms-change max change #iterations 0.1110138 17.23772 at 10iterations 9.8818522E-03 1.475437 at 20iterations 1.8689389E-03 0.2885246 at 30iterations 6.9804175E-04 0.1133289 at 40iterations 2.7961613E-04 4.6363831E-02 at 50iterations finished qdiffx linear iterations at : 07:17:55 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 2.7961613E-04 4.6363831E-02 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 07:17:56 4.581u 0.390s 0:05.47 90.8% 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 07:17:56 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 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: 1.751135 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): 0.4169999 49.96400 ymin,ymax (A): -8.383000 52.60600 zmin,zma (A): 1.254000 60.70900 x,y,z range (A): 49.54700 60.98900 59.45500 scale (grids/A): 1.751135 object centre (A): 25.19050 22.11150 30.98150 number of atom coordinates read : 3424 total number of charged atoms : 3273 net assigned charge : 7.8380108E-06 assigned positive charge : 515.9973 centred at (gu) : 88.78954 87.56068 91.55124 assigned negative charge : -515.9987 centred at (gu) : 88.50174 87.50635 91.55728 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27679 grid for indexing accessible points = 1.400000 m= 28260 mr = 59487 m= 3399 mr = 20588 m= 122 mr = 1937 m= 4 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 791 time to turn everything in is 0.6800000 number of dielectric boundary points 33284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 25443 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) : 0.5837118 object centre at (A) : 25.19050 22.11150 30.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3062079E-02 1.4059490E-03 midg,1,midg; midg,igrid,midg -1.7719077E-02 -1.8573640E-02 1,midg,midg; igrid,midg,midg -5.7406095E-03 9.0228915E-03 gauss-seidel spectral radius is 0.9984664 estimated iterations to convergence 203 setup time was (sec) 0.9700000 now iterating at: 07:17:57 rms-change max change #iterations 4.223442 191.1119 at 10iterations 1.886882 61.33146 at 20iterations 0.8477570 25.18591 at 30iterations 0.3799627 13.65747 at 40iterations 0.1712867 5.248771 at 50iterations 7.7019915E-02 2.450250 at 60iterations 3.4726854E-02 1.068928 at 70iterations 1.5810480E-02 0.5156975 at 80iterations 7.4130739E-03 0.2543201 at 90iterations 3.6730105E-03 0.1254654 at 100iterations 2.0031510E-03 7.3457718E-02 at 110iterations 1.2265070E-03 4.1110992E-02 at 120iterations finished qdiffx linear iterations at : 07:18:07 total time elapsed so far: 10.75000 # loops : 120 mean,max change (kT/e) : 1.2265070E-03 4.1110992E-02 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.92000 DelPhi exited at 07:18:08 10.929u 0.428s 0:12.05 94.1% 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 07:18:08 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 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: 2.626703 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): 0.4169999 49.96400 ymin,ymax (A): -8.383000 52.60600 zmin,zma (A): 1.254000 60.70900 x,y,z range (A): 49.54700 60.98900 59.45500 scale (grids/A): 2.626703 object centre (A): 25.19050 22.11150 30.98150 number of atom coordinates read : 3424 total number of charged atoms : 3273 net assigned charge : 7.8380108E-06 assigned positive charge : 515.9973 centred at (gu) : 88.18407 86.34084 92.32658 assigned negative charge : -515.9987 centred at (gu) : 87.75249 86.25961 92.33583 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 193703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27679 grid for indexing accessible points = 1.400000 m= 95383 mr = 144208 m= 29982 mr = 78033 m= 5699 mr = 23674 m= 579 mr = 4052 m= 15 mr = 312 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 2767 time to turn everything in is 1.760000 number of dielectric boundary points 75081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 26170 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) : 1.751135 object centre at (A) : 25.19050 22.11150 30.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2141822 -0.1365450 midg,1,midg; midg,igrid,midg -0.2569171 -0.2936888 1,midg,midg; igrid,midg,midg -7.4330665E-02 0.1145031 gauss-seidel spectral radius is 0.9992260 estimated iterations to convergence 284 setup time was (sec) 2.090000 now iterating at: 07:18:11 rms-change max change #iterations 10.29113 279.3289 at 10iterations 5.959086 134.2646 at 20iterations 3.425071 68.23842 at 30iterations 1.962578 38.10373 at 40iterations 1.121296 21.07100 at 50iterations 0.6398132 10.92716 at 60iterations 0.3654136 6.780714 at 70iterations 0.2082501 3.915026 at 80iterations 0.1188071 2.497066 at 90iterations 6.7679301E-02 1.231728 at 100iterations 3.8651947E-02 0.7492008 at 110iterations 2.2069486E-02 0.3923583 at 120iterations 1.2668822E-02 0.2170486 at 130iterations 7.3663718E-03 0.1242142 at 140iterations 4.3857992E-03 8.4228516E-02 at 150iterations 2.7062334E-03 4.9106598E-02 at 160iterations 1.7692369E-03 3.5781860E-02 at 170iterations 1.2402605E-03 2.6103973E-02 at 180iterations finished qdiffx linear iterations at : 07:18:27 total time elapsed so far: 18.41000 # loops : 180 mean,max change (kT/e) : 1.2402605E-03 2.6103973E-02 energy calculations done at 18.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.58000 DelPhi exited at 07:18:28 18.580u 0.438s 0:19.40 97.9% 0+0k 0+0io 0pf+0w