Sat Oct 8 20:47:22 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 20:47:22 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 = 2577 !!! 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: ZN4 427 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: 0.6213239 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): -10.82200 38.64300 ymin,ymax (A): -22.24500 24.50500 zmin,zma (A): -12.60000 44.69700 x,y,z range (A): 49.46500 46.75000 57.29700 scale (grids/A): 0.6213239 object centre (A): 13.91050 1.130000 16.04850 number of atom coordinates read : 2577 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.6440 centred at (gu) : 88.60161 89.39175 89.82166 assigned negative charge : -388.7386 centred at (gu) : 88.51054 89.43988 89.69419 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6606 nv = 96 ne = 84 npr = 53304 no. pairs analyzed = 53304 no. exposed pairs = 2980 no. arc points = 21228 no. surface atoms = 1003 nbur = 1574 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 3725 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 94 time to turn everything in is 0.3400000 number of dielectric boundary points 3142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2189 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7873795E-09 1.1577926E-08 midg,1,midg; midg,igrid,midg 7.6260305E-09 4.7280700E-11 1,midg,midg; igrid,midg,midg -4.1631418E-09 7.0692128E-09 gauss-seidel spectral radius is 0.9865795 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 20:47:23 rms-change max change #iterations 0.1294998 19.83338 at 10iterations 1.1932336E-02 1.812721 at 20iterations 1.1122876E-03 0.1506805 at 30iterations 1.0264541E-04 1.5991211E-02 at 40iterations 9.6016947E-06 1.6021729E-03 at 50iterations finished qdiffx linear iterations at : 20:47:27 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 9.6016947E-06 1.6021729E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 20:47:27 4.062u 0.266s 0:04.64 93.1% 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 20:47:27 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 = 2577 !!! 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: ZN4 427 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: 1.863972 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): -10.82200 38.64300 ymin,ymax (A): -22.24500 24.50500 zmin,zma (A): -12.60000 44.69700 x,y,z range (A): 49.46500 46.75000 57.29700 scale (grids/A): 1.863972 object centre (A): 13.91050 1.130000 16.04850 number of atom coordinates read : 2577 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.6440 centred at (gu) : 85.80448 88.17471 89.46472 assigned negative charge : -388.7386 centred at (gu) : 85.53130 88.31964 89.08249 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21228 grid for indexing accessible points = 1.400000 m= 25026 mr = 50725 m= 3305 mr = 18596 m= 167 mr = 2013 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 4166 time to turn everything in is 0.6300000 number of dielectric boundary points 28972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19208 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) : 0.6213239 object centre at (A) : 13.91050 1.130000 16.04850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6280061E-02 2.1404680E-02 midg,1,midg; midg,igrid,midg 1.2327292E-02 1.1887309E-03 1,midg,midg; igrid,midg,midg -3.4581241E-03 3.2094616E-02 gauss-seidel spectral radius is 0.9985707 estimated iterations to convergence 210 setup time was (sec) 0.9300000 now iterating at: 20:47:28 rms-change max change #iterations 4.084607 193.1297 at 10iterations 1.876241 59.63630 at 20iterations 0.8643754 28.35398 at 30iterations 0.3978959 14.29150 at 40iterations 0.1832900 6.123091 at 50iterations 8.4245764E-02 3.188442 at 60iterations 3.8815767E-02 1.266113 at 70iterations 1.7847521E-02 0.6108665 at 80iterations 8.2270941E-03 0.2671165 at 90iterations 3.7908321E-03 0.1286249 at 100iterations 1.7400919E-03 5.8620453E-02 at 110iterations 8.0377457E-04 2.6872635E-02 at 120iterations finished qdiffx linear iterations at : 20:47:36 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 8.0377457E-04 2.6872635E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 20:47:37 9.326u 0.289s 0:09.92 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 Sat Oct 8 2011 at 20:47:37 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 = 2577 !!! 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: ZN4 427 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: 2.795958 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): -10.82200 38.64300 ymin,ymax (A): -22.24500 24.50500 zmin,zma (A): -12.60000 44.69700 x,y,z range (A): 49.46500 46.75000 57.29700 scale (grids/A): 2.795958 object centre (A): 13.91050 1.130000 16.04850 number of atom coordinates read : 2577 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.6440 centred at (gu) : 83.70675 87.26193 89.19695 assigned negative charge : -388.7386 centred at (gu) : 83.29683 87.47945 88.62358 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 166029 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21228 grid for indexing accessible points = 1.400000 m= 83461 mr = 122203 m= 27592 mr = 69076 m= 5851 mr = 22168 m= 695 mr = 4352 m= 39 mr = 464 m= 0 mr = 16 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 14542 time to turn everything in is 1.580000 number of dielectric boundary points 65388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19595 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) : 1.863972 object centre at (A) : 13.91050 1.130000 16.04850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2685214E-02 0.2676426 midg,1,midg; midg,igrid,midg 0.1539979 3.1201607E-03 1,midg,midg; igrid,midg,midg -3.5396513E-02 0.4274442 gauss-seidel spectral radius is 0.9992343 estimated iterations to convergence 285 setup time was (sec) 1.890000 now iterating at: 20:47:39 rms-change max change #iterations 9.491826 303.0406 at 10iterations 5.435445 106.4784 at 20iterations 3.096405 57.63188 at 30iterations 1.765936 35.09388 at 40iterations 1.006429 18.62984 at 50iterations 0.5714560 10.77149 at 60iterations 0.3259012 6.542526 at 70iterations 0.1852922 3.345028 at 80iterations 0.1053594 2.099073 at 90iterations 5.9840515E-02 1.054838 at 100iterations 3.3871654E-02 0.5871239 at 110iterations 1.9355169E-02 0.3803124 at 120iterations 1.1015321E-02 0.2018471 at 130iterations 6.2407632E-03 0.1146736 at 140iterations 3.5485048E-03 6.4685822E-02 at 150iterations 2.0158535E-03 3.6550522E-02 at 160iterations 1.1495764E-03 2.2812843E-02 at 170iterations 6.5200322E-04 1.2452364E-02 at 180iterations finished qdiffx linear iterations at : 20:47:53 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 6.5200322E-04 1.2452364E-02 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 20:47:53 15.487u 0.329s 0:16.08 98.2% 0+0k 0+0io 0pf+0w