Mon Oct 10 14:04:18 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 Mon Oct 10 2011 at 14:04:19 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3278 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5579937 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): -9.788000 42.07400 ymin,ymax (A): -38.51900 25.28100 zmin,zma (A): -15.62100 34.01600 x,y,z range (A): 51.86200 63.80000 49.63700 scale (grids/A): 0.5579937 object centre (A): 16.14300 -6.619000 9.197500 number of atom coordinates read : 3278 total number of charged atoms : 3134 net assigned charge : 5.6475401E-06 assigned positive charge : 488.7547 centred at (gu) : 89.99876 91.79535 90.43595 assigned negative charge : -488.7561 centred at (gu) : 90.02023 91.74120 90.39563 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6608 nv = 96 ne = 84 npr = 67701 no. pairs analyzed = 67701 no. exposed pairs = 3894 no. arc points = 27440 no. surface atoms = 1326 nbur = 1952 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= 266 mr = 3645 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2766 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8572 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2430179E-10 4.8908533E-10 midg,1,midg; midg,igrid,midg -4.0665743E-10 9.2920832E-10 1,midg,midg; igrid,midg,midg 2.2767320E-10 -2.5760552E-10 gauss-seidel spectral radius is 0.9834513 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 14:04:19 rms-change max change #iterations 8.6088367E-02 14.73026 at 10iterations 6.1603002E-03 0.9390402 at 20iterations 4.8558161E-04 8.0413818E-02 at 30iterations 5.5526267E-05 9.2191696E-03 at 40iterations 1.1240217E-05 2.0370483E-03 at 50iterations finished qdiffx linear iterations at : 14:04:22 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.1240217E-05 2.0370483E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:04:22 3.398u 0.150s 0:03.95 89.6% 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 14:04:23 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3278 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.673981 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): -9.788000 42.07400 ymin,ymax (A): -38.51900 25.28100 zmin,zma (A): -15.62100 34.01600 x,y,z range (A): 51.86200 63.80000 49.63700 scale (grids/A): 1.673981 object centre (A): 16.14300 -6.619000 9.197500 number of atom coordinates read : 3278 total number of charged atoms : 3134 net assigned charge : 5.6475401E-06 assigned positive charge : 488.7547 centred at (gu) : 89.99562 95.38520 91.30695 assigned negative charge : -488.7561 centred at (gu) : 90.06039 95.22327 91.18652 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27440 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23566 mr = 51451 m= 2426 mr = 16739 m= 72 mr = 1237 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 440 time to turn everything in is 0.3500000 number of dielectric boundary points 29929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 24155 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) : 0.5579937 object centre at (A) : 16.14300 -6.619000 9.197500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9049079E-03 4.1272431E-03 midg,1,midg; midg,igrid,midg 8.9657251E-03 5.8235745E-03 1,midg,midg; igrid,midg,midg 4.9848887E-03 9.8311028E-04 gauss-seidel spectral radius is 0.9982963 estimated iterations to convergence 192 setup time was (sec) 0.5600000 now iterating at: 14:04:23 rms-change max change #iterations 3.677129 162.3365 at 10iterations 1.569337 56.88140 at 20iterations 0.6760160 24.50239 at 30iterations 0.2895302 9.810963 at 40iterations 0.1244843 4.410347 at 50iterations 5.3436745E-02 1.819688 at 60iterations 2.2944024E-02 0.7410073 at 70iterations 9.8402854E-03 0.3429565 at 80iterations 4.2327833E-03 0.1602468 at 90iterations 1.8210507E-03 6.0127258E-02 at 100iterations 7.8558008E-04 2.7201653E-02 at 110iterations 3.4010771E-04 1.1013031E-02 at 120iterations finished qdiffx linear iterations at : 14:04:30 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 3.4010771E-04 1.1013031E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 14:04:31 7.652u 0.196s 0:08.38 93.5% 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 14:04:31 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3278 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.510972 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): -9.788000 42.07400 ymin,ymax (A): -38.51900 25.28100 zmin,zma (A): -15.62100 34.01600 x,y,z range (A): 51.86200 63.80000 49.63700 scale (grids/A): 2.510972 object centre (A): 16.14300 -6.619000 9.197500 number of atom coordinates read : 3278 total number of charged atoms : 3134 net assigned charge : 5.6475401E-06 assigned positive charge : 488.7547 centred at (gu) : 89.99325 98.07745 91.96014 assigned negative charge : -488.7561 centred at (gu) : 90.09056 97.83482 91.77972 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 170360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27440 grid for indexing accessible points = 1.400000 m= 81240 mr = 125358 m= 23498 mr = 65663 m= 3894 mr = 18128 m= 305 mr = 2548 m= 10 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1455 time to turn everything in is 0.8600000 number of dielectric boundary points 67504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 25051 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) : 1.673981 object centre at (A) : 16.14300 -6.619000 9.197500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1300900 7.0887171E-02 midg,1,midg; midg,igrid,midg 0.2077576 2.1317914E-02 1,midg,midg; igrid,midg,midg 9.1457456E-02 2.8455546E-02 gauss-seidel spectral radius is 0.9991723 estimated iterations to convergence 275 setup time was (sec) 1.090000 now iterating at: 14:04:32 rms-change max change #iterations 9.279268 284.4740 at 10iterations 5.241805 114.7319 at 20iterations 2.953757 73.73481 at 30iterations 1.658775 32.36385 at 40iterations 0.9275795 17.60319 at 50iterations 0.5177247 11.80343 at 60iterations 0.2898294 5.688572 at 70iterations 0.1617303 3.199471 at 80iterations 9.0132080E-02 2.033842 at 90iterations 5.0292354E-02 0.9486923 at 100iterations 2.7998239E-02 0.5441195 at 110iterations 1.5581177E-02 0.2913609 at 120iterations 8.6997105E-03 0.1714582 at 130iterations 4.8405146E-03 9.3481064E-02 at 140iterations 2.7024806E-03 5.4176331E-02 at 150iterations 1.5084598E-03 2.6977539E-02 at 160iterations 8.4388279E-04 1.8215179E-02 at 170iterations 4.7427046E-04 1.0576904E-02 at 180iterations finished qdiffx linear iterations at : 14:04:43 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 4.7427046E-04 1.0576904E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 14:04:44 12.297u 0.200s 0:12.81 97.5% 0+0k 0+0io 0pf+0w