Mon Oct 10 16:04:19 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+sph.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 = amb.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 Mon Oct 10 2011 at 16:04:19 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 890 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: 0.5491539 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): 7.344000 59.03000 ymin,ymax (A): -29.60600 34.20100 zmin,zma (A): -29.26800 35.55900 x,y,z range (A): 51.68600 63.80700 64.82700 scale (grids/A): 0.5491539 object centre (A): 33.18700 2.297501 3.145501 number of atom coordinates read : 4299 total number of charged atoms : 4206 net assigned charge : 5.700017 assigned positive charge : 651.3319 centred at (gu) : 89.86213 89.55831 88.62981 assigned negative charge : -645.6354 centred at (gu) : 89.87281 89.52039 88.65019 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8500 nv = 96 ne = 84 npr = 86035 no. pairs analyzed = 86035 no. exposed pairs = 5417 no. arc points = 36745 no. surface atoms = 1827 nbur = 2472 mkacc time = 0.1500000 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 = 1.568000 m= 338 mr = 4589 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2900000 number of dielectric boundary points 4231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3696 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 11165 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6652813E-10 1.3096904E-10 midg,1,midg; midg,igrid,midg -1.7861773E-11 7.2565481E-10 1,midg,midg; igrid,midg,midg 5.3219368E-10 2.7420885E-10 gauss-seidel spectral radius is 0.9830012 estimated iterations to convergence 63 setup time was (sec) 0.4800000 now iterating at: 16:04:20 rms-change max change #iterations 9.1056019E-02 13.28728 at 10iterations 6.5298830E-03 0.8710938 at 20iterations 7.1952428E-04 0.1259632 at 30iterations 2.0864484E-04 3.0443192E-02 at 40iterations 8.1952319E-05 1.1258602E-02 at 50iterations finished qdiffx linear iterations at : 16:04:23 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 8.1952319E-05 1.1258602E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 16:04:23 3.546u 0.180s 0:04.11 90.5% 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 Mon Oct 10 2011 at 16:04:23 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 890 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: 1.647462 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): 7.344000 59.03000 ymin,ymax (A): -29.60600 34.20100 zmin,zma (A): -29.26800 35.55900 x,y,z range (A): 51.68600 63.80700 64.82700 scale (grids/A): 1.647462 object centre (A): 33.18700 2.297501 3.145501 number of atom coordinates read : 4299 total number of charged atoms : 4206 net assigned charge : 5.700017 assigned positive charge : 651.3319 centred at (gu) : 89.58486 88.67348 85.88805 assigned negative charge : -645.6354 centred at (gu) : 89.61800 88.56093 85.95010 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 94820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36745 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30725 mr = 66794 m= 3382 mr = 21422 m= 88 mr = 1677 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 577 time to turn everything in is 0.4700000 number of dielectric boundary points 39113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 386 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 32257 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) : 0.5491539 object centre at (A) : 33.18700 2.297501 3.145501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7139478E-02 -4.7693471E-03 midg,1,midg; midg,igrid,midg 1.2624893E-02 9.7302701E-03 1,midg,midg; igrid,midg,midg 4.1891970E-03 -1.0247458E-03 gauss-seidel spectral radius is 0.9983563 estimated iterations to convergence 196 setup time was (sec) 0.6900000 now iterating at: 16:04:24 rms-change max change #iterations 4.201806 154.4166 at 10iterations 1.821383 62.64943 at 20iterations 0.7964799 22.58463 at 30iterations 0.3467242 10.44359 at 40iterations 0.1512841 4.665564 at 50iterations 6.5940790E-02 1.985020 at 60iterations 2.8871115E-02 0.8602915 at 70iterations 1.2637225E-02 0.3643707 at 80iterations 5.5456669E-03 0.1634197 at 90iterations 2.4728677E-03 7.6798886E-02 at 100iterations 1.1338203E-03 3.9306641E-02 at 110iterations 5.5655657E-04 1.7302990E-02 at 120iterations finished qdiffx linear iterations at : 16:04:31 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 5.5655657E-04 1.7302990E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 16:04:32 8.092u 0.209s 0:08.57 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 Mon Oct 10 2011 at 16:04:32 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 890 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: 2.471192 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): 7.344000 59.03000 ymin,ymax (A): -29.60600 34.20100 zmin,zma (A): -29.26800 35.55900 x,y,z range (A): 51.68600 63.80700 64.82700 scale (grids/A): 2.471192 object centre (A): 33.18700 2.297501 3.145501 number of atom coordinates read : 4299 total number of charged atoms : 4206 net assigned charge : 5.700017 assigned positive charge : 651.3319 centred at (gu) : 89.37698 88.00979 83.83167 assigned negative charge : -645.6354 centred at (gu) : 89.42695 87.84133 83.92502 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 220572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36745 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105356 mr = 163384 m= 31296 mr = 83918 m= 5363 mr = 23719 m= 374 mr = 3551 m= 6 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 1957 time to turn everything in is 1.130000 number of dielectric boundary points 88247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 33616 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) : 1.647462 object centre at (A) : 33.18700 2.297501 3.145501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4215834 -0.1076378 midg,1,midg; midg,igrid,midg 0.3185858 0.1088701 1,midg,midg; igrid,midg,midg 5.2735195E-02 -4.9861455E-03 gauss-seidel spectral radius is 0.9992262 estimated iterations to convergence 284 setup time was (sec) 1.370000 now iterating at: 16:04:33 rms-change max change #iterations 10.85888 304.3109 at 10iterations 6.374094 158.0291 at 20iterations 3.715793 93.07793 at 30iterations 2.156922 42.65480 at 40iterations 1.245714 23.42205 at 50iterations 0.7171342 13.20912 at 60iterations 0.4112546 7.472510 at 70iterations 0.2360984 4.198563 at 80iterations 0.1352709 2.389258 at 90iterations 7.7441156E-02 1.339682 at 100iterations 4.4258021E-02 0.7574310 at 110iterations 2.5251986E-02 0.4474821 at 120iterations 1.4406206E-02 0.2425823 at 130iterations 8.2576908E-03 0.1537390 at 140iterations 4.7314507E-03 8.5029602E-02 at 150iterations 2.7259407E-03 4.6690941E-02 at 160iterations 1.5915509E-03 3.2513618E-02 at 170iterations 9.4957114E-04 1.7025948E-02 at 180iterations finished qdiffx linear iterations at : 16:04:45 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 9.4957114E-04 1.7025948E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 16:04:46 13.096u 0.215s 0:13.83 96.1% 0+0k 0+0io 0pf+0w