Mon Oct 10 21:31:30 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 21:31:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 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: 0.5576354 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): -2.049000 51.07400 ymin,ymax (A): -15.29700 41.39500 zmin,zma (A): 28.06100 91.90200 x,y,z range (A): 53.12300 56.69200 63.84100 scale (grids/A): 0.5576354 object centre (A): 24.51250 13.04900 59.98150 number of atom coordinates read : 2837 total number of charged atoms : 2765 net assigned charge : 1.500008 assigned positive charge : 420.8341 centred at (gu) : 92.32278 89.23412 90.94508 assigned negative charge : -419.3355 centred at (gu) : 92.24294 89.31072 90.85538 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5912 nv = 96 ne = 84 npr = 55102 no. pairs analyzed = 55102 no. exposed pairs = 4011 no. arc points = 27924 no. surface atoms = 1340 nbur = 1497 mkacc time = 0.1100000 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 = 1.540000 m= 226 mr = 2814 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2817 ## 318 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7717 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9656985E-10 1.2072260E-09 midg,1,midg; midg,igrid,midg 1.0068849E-09 -5.1797883E-10 1,midg,midg; igrid,midg,midg -3.7140380E-10 1.5393201E-09 gauss-seidel spectral radius is 0.9834135 estimated iterations to convergence 64 setup time was (sec) 0.5400000 now iterating at: 21:31:31 rms-change max change #iterations 7.6774664E-02 15.18460 at 10iterations 5.4246415E-03 0.9843969 at 20iterations 4.5105311E-04 6.4331055E-02 at 30iterations 6.0498114E-05 8.4381104E-03 at 40iterations 1.1823296E-05 1.4305115E-03 at 50iterations finished qdiffx linear iterations at : 21:31:34 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1823296E-05 1.4305115E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 21:31:35 3.384u 0.218s 0:04.27 84.0% 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 21:31:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 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: 1.672906 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): -2.049000 51.07400 ymin,ymax (A): -15.29700 41.39500 zmin,zma (A): 28.06100 91.90200 x,y,z range (A): 53.12300 56.69200 63.84100 scale (grids/A): 1.672906 object centre (A): 24.51250 13.04900 59.98150 number of atom coordinates read : 2837 total number of charged atoms : 2765 net assigned charge : 1.500008 assigned positive charge : 420.8341 centred at (gu) : 96.96776 87.70165 92.83452 assigned negative charge : -419.3355 centred at (gu) : 96.72852 87.93186 92.56572 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65143 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27924 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19606 mr = 42321 m= 2190 mr = 12894 m= 60 mr = 1037 m= 0 mr = 7 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 30740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 21283 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) : 0.5576354 object centre at (A) : 24.51250 13.04900 59.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7016860E-02 9.1064442E-03 midg,1,midg; midg,igrid,midg 1.9032153E-05 -8.8644400E-03 1,midg,midg; igrid,midg,midg 3.0721461E-03 2.6406687E-02 gauss-seidel spectral radius is 0.9982705 estimated iterations to convergence 191 setup time was (sec) 0.7700000 now iterating at: 21:31:36 rms-change max change #iterations 3.346131 171.9169 at 10iterations 1.417492 57.91858 at 20iterations 0.6030189 22.30436 at 30iterations 0.2552018 10.09220 at 40iterations 0.1087984 3.824318 at 50iterations 4.6323929E-02 1.651461 at 60iterations 1.9742899E-02 0.7753067 at 70iterations 8.3984258E-03 0.3045921 at 80iterations 3.5484852E-03 0.1234818 at 90iterations 1.5262587E-03 5.2804947E-02 at 100iterations 6.5099268E-04 2.2112206E-02 at 110iterations 2.7996677E-04 9.8419189E-03 at 120iterations finished qdiffx linear iterations at : 21:31:42 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 2.7996677E-04 9.8419189E-03 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 21:31:43 7.585u 0.233s 0:08.39 93.0% 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 21:31:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 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: 2.509359 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): -2.049000 51.07400 ymin,ymax (A): -15.29700 41.39500 zmin,zma (A): 28.06100 91.90200 x,y,z range (A): 53.12300 56.69200 63.84100 scale (grids/A): 2.509359 object centre (A): 24.51250 13.04900 59.98150 number of atom coordinates read : 2837 total number of charged atoms : 2765 net assigned charge : 1.500008 assigned positive charge : 420.8341 centred at (gu) : 100.4515 86.55219 94.25156 assigned negative charge : -419.3355 centred at (gu) : 100.0928 86.89780 93.84850 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 151387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27924 grid for indexing accessible points = 1.400000 m= 66924 mr = 104403 m= 19830 mr = 51173 m= 3380 mr = 14494 m= 229 mr = 2149 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 69458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 22102 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) : 1.672906 object centre at (A) : 24.51250 13.04900 59.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5784140 0.1696594 midg,1,midg; midg,igrid,midg -5.0867338E-02 -0.1394083 1,midg,midg; igrid,midg,midg 7.5077564E-02 0.3642825 gauss-seidel spectral radius is 0.9991671 estimated iterations to convergence 274 setup time was (sec) 1.460000 now iterating at: 21:31:45 rms-change max change #iterations 8.729060 362.8428 at 10iterations 4.977588 132.0463 at 20iterations 2.817900 63.45337 at 30iterations 1.587613 36.93126 at 40iterations 0.8931782 21.07694 at 50iterations 0.5000777 11.55692 at 60iterations 0.2793649 5.820464 at 70iterations 0.1558825 3.340732 at 80iterations 8.6904436E-02 1.940067 at 90iterations 4.8403345E-02 0.9693909 at 100iterations 2.6903592E-02 0.6892891 at 110iterations 1.4989154E-02 0.2896862 at 120iterations 8.3430121E-03 0.1655464 at 130iterations 4.6391822E-03 9.1735840E-02 at 140iterations 2.5785330E-03 5.2490473E-02 at 150iterations 1.4351991E-03 3.1335354E-02 at 160iterations 7.9955364E-04 1.6835213E-02 at 170iterations 4.4607703E-04 9.7503662E-03 at 180iterations finished qdiffx linear iterations at : 21:31:55 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 4.4607703E-04 9.7503662E-03 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 21:31:56 12.276u 0.257s 0:13.31 94.0% 0+0k 0+0io 0pf+0w