Mon Oct 10 10:41:56 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 10:41:56 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5267 !!! WARNING: ADP 1560 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5299512 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): -10.17400 57.00200 ymin,ymax (A): -49.59200 12.48400 zmin,zma (A): -19.38700 46.32300 x,y,z range (A): 67.17600 62.07600 65.71000 scale (grids/A): 0.5299512 object centre (A): 23.41400 -18.55400 13.46800 number of atom coordinates read : 5267 total number of charged atoms : 5112 net assigned charge : 9.000014 assigned positive charge : 833.6914 centred at (gu) : 89.10910 90.89611 88.95050 assigned negative charge : -824.6987 centred at (gu) : 89.08765 90.95028 89.01627 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9616 nv = 96 ne = 84 npr = 104033 no. pairs analyzed = 104033 no. exposed pairs = 6409 no. arc points = 43209 no. surface atoms = 2143 nbur = 3124 mkacc time = 0.2700000 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 = 1.624000 m= 348 mr = 5372 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.5500000 number of dielectric boundary points 4582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4369 ## 585 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 12692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4826302E-10 -1.0941519E-10 midg,1,midg; midg,igrid,midg 5.1812776E-10 -9.0797453E-11 1,midg,midg; igrid,midg,midg 1.8557447E-10 3.4798450E-10 gauss-seidel spectral radius is 0.9818180 estimated iterations to convergence 61 setup time was (sec) 0.8600000 now iterating at: 10:41:57 rms-change max change #iterations 8.7069348E-02 11.24800 at 10iterations 5.6037181E-03 0.8960190 at 20iterations 7.7506097E-04 0.1059170 at 30iterations 3.6982051E-04 5.2039146E-02 at 40iterations 2.0036091E-04 2.7970314E-02 at 50iterations finished qdiffx linear iterations at : 10:42:01 total time elapsed so far: 4.830000 # loops : 50 mean,max change (kT/e) : 2.0036091E-04 2.7970314E-02 energy calculations done at 4.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.010000 DelPhi exited at 10:42:02 5.019u 0.386s 0:05.75 93.7% 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 10:42:02 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5267 !!! WARNING: ADP 1560 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.589853 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): -10.17400 57.00200 ymin,ymax (A): -49.59200 12.48400 zmin,zma (A): -19.38700 46.32300 x,y,z range (A): 67.17600 62.07600 65.71000 scale (grids/A): 1.589853 object centre (A): 23.41400 -18.55400 13.46800 number of atom coordinates read : 5267 total number of charged atoms : 5112 net assigned charge : 9.000014 assigned positive charge : 833.6914 centred at (gu) : 87.32551 92.68687 86.85001 assigned negative charge : -824.6987 centred at (gu) : 87.26310 92.85068 87.04864 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 108734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43209 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 34395 mr = 77906 m= 3280 mr = 24257 m= 60 mr = 1526 m= 0 mr = 7 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2917 time to turn everything in is 0.8600000 number of dielectric boundary points 42773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 542 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 38788 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) : 0.5299512 object centre at (A) : 23.41400 -18.55400 13.46800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5448927E-03 -4.8775285E-02 midg,1,midg; midg,igrid,midg 1.0437791E-02 3.1052234E-03 1,midg,midg; igrid,midg,midg 4.4604074E-03 3.0047633E-02 gauss-seidel spectral radius is 0.9983004 estimated iterations to convergence 193 setup time was (sec) 1.170000 now iterating at: 10:42:03 rms-change max change #iterations 4.474375 189.2220 at 10iterations 1.918075 58.55202 at 20iterations 0.8246517 24.69253 at 30iterations 0.3548089 10.55997 at 40iterations 0.1526722 4.080608 at 50iterations 6.5450117E-02 2.058853 at 60iterations 2.8259672E-02 0.8346386 at 70iterations 1.2233767E-02 0.3747940 at 80iterations 5.3162440E-03 0.1542206 at 90iterations 2.3649537E-03 7.0687294E-02 at 100iterations 1.1230002E-03 4.1603088E-02 at 110iterations 6.1110203E-04 2.1302223E-02 at 120iterations finished qdiffx linear iterations at : 10:42:13 total time elapsed so far: 11.11000 # loops : 120 mean,max change (kT/e) : 6.1110203E-04 2.1302223E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 10:42:14 11.277u 0.453s 0:11.99 97.7% 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 10:42:14 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5267 !!! WARNING: ADP 1560 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.384780 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): -10.17400 57.00200 ymin,ymax (A): -49.59200 12.48400 zmin,zma (A): -19.38700 46.32300 x,y,z range (A): 67.17600 62.07600 65.71000 scale (grids/A): 2.384780 object centre (A): 23.41400 -18.55400 13.46800 number of atom coordinates read : 5267 total number of charged atoms : 5112 net assigned charge : 9.000014 assigned positive charge : 833.6914 centred at (gu) : 85.98779 94.03004 85.27459 assigned negative charge : -824.6987 centred at (gu) : 85.89455 94.27576 85.57307 start vw surface at 0.1700000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 252894 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43209 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 121767 mr = 190082 m= 33221 mr = 98069 m= 5010 mr = 25029 m= 283 mr = 3191 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 10268 time to turn everything in is 2.280000 number of dielectric boundary points 96688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 2.430000 number of grid points assigned charge 40830 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) : 1.589853 object centre at (A) : 23.41400 -18.55400 13.46800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1633380E-03 -1.177728 midg,1,midg; midg,igrid,midg 0.1271453 -3.4827527E-02 1,midg,midg; igrid,midg,midg 0.1228433 0.6285316 gauss-seidel spectral radius is 0.9992202 estimated iterations to convergence 283 setup time was (sec) 2.640000 now iterating at: 10:42:17 rms-change max change #iterations 11.74294 497.9490 at 10iterations 6.859128 145.5805 at 20iterations 3.983949 86.42680 at 30iterations 2.295073 53.18461 at 40iterations 1.322031 25.05905 at 50iterations 0.7583287 14.68372 at 60iterations 0.4332514 8.665394 at 70iterations 0.2472003 4.457846 at 80iterations 0.1409744 2.614784 at 90iterations 8.0323532E-02 1.394658 at 100iterations 4.5673501E-02 0.7710152 at 110iterations 2.5966572E-02 0.4374790 at 120iterations 1.4743008E-02 0.2709889 at 130iterations 8.3710467E-03 0.1574669 at 140iterations 4.7531938E-03 7.8879833E-02 at 150iterations 2.7039358E-03 4.3479919E-02 at 160iterations 1.5387879E-03 2.4806976E-02 at 170iterations 8.7700528E-04 1.5351295E-02 at 180iterations finished qdiffx linear iterations at : 10:42:35 total time elapsed so far: 21.04000 # loops : 180 mean,max change (kT/e) : 8.7700528E-04 1.5351295E-02 energy calculations done at 21.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.22000 DelPhi exited at 10:42:36 21.222u 0.481s 0:21.99 98.6% 0+0k 0+0io 0pf+0w