Sun Oct 9 15:04:45 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 Sun Oct 9 2011 at 15:04:45 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2927 !!! WARNING: HIT 110 has a net charge of 0.5140 !!! WARNING: HIT 112 has a net charge of 0.5140 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: 0.5633357 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): 0.8360001 49.32900 ymin,ymax (A): -17.14500 31.50400 zmin,zma (A): 124.5990 187.7940 x,y,z range (A): 48.49300 48.64900 63.19501 scale (grids/A): 0.5633357 object centre (A): 25.08250 7.179500 156.1965 number of atom coordinates read : 2927 total number of charged atoms : 2786 net assigned charge : 8.528022 assigned positive charge : 440.6283 centred at (gu) : 90.60570 89.54994 89.23402 assigned negative charge : -432.1013 centred at (gu) : 90.60521 89.60545 89.28005 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6297 nv = 96 ne = 84 npr = 57226 no. pairs analyzed = 57226 no. exposed pairs = 3873 no. arc points = 27507 no. surface atoms = 1280 nbur = 1647 mkacc time = 0.1000000 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= 262 mr = 3223 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2840 ## 344 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8866519E-09 3.8673395E-10 midg,1,midg; midg,igrid,midg 1.8760864E-09 3.1008479E-10 1,midg,midg; igrid,midg,midg 8.7899005E-10 1.1792299E-09 gauss-seidel spectral radius is 0.9837475 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 15:04:46 rms-change max change #iterations 8.5499257E-02 14.39340 at 10iterations 6.2321359E-03 0.8933544 at 20iterations 4.5062701E-04 6.3362122E-02 at 30iterations 3.4430261E-05 5.0697327E-03 at 40iterations 3.0333445E-06 4.4631958E-04 at 50iterations finished qdiffx linear iterations at : 15:04:49 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.0333445E-06 4.4631958E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 15:04:49 3.429u 0.164s 0:03.90 91.7% 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 Sun Oct 9 2011 at 15:04:49 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2927 !!! WARNING: HIT 110 has a net charge of 0.5140 !!! WARNING: HIT 112 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.690007 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): 0.8360001 49.32900 ymin,ymax (A): -17.14500 31.50400 zmin,zma (A): 124.5990 187.7940 x,y,z range (A): 48.49300 48.64900 63.19501 scale (grids/A): 1.690007 object centre (A): 25.08250 7.179500 156.1965 number of atom coordinates read : 2927 total number of charged atoms : 2786 net assigned charge : 8.528022 assigned positive charge : 440.6283 centred at (gu) : 91.81647 88.64914 87.70141 assigned negative charge : -432.1013 centred at (gu) : 91.81544 88.81617 87.83993 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27507 grid for indexing accessible points = 1.400000 m= 22179 mr = 45879 m= 2580 mr = 15394 m= 80 mr = 1341 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 99 time to turn everything in is 0.3500000 number of dielectric boundary points 30957 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 307 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21507 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) : 0.5633357 object centre at (A) : 25.08250 7.179500 156.1965 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9098244E-03 1.6348783E-02 midg,1,midg; midg,igrid,midg 4.3879556E-03 -2.2279595E-03 1,midg,midg; igrid,midg,midg 9.6786395E-03 1.3056518E-02 gauss-seidel spectral radius is 0.9983117 estimated iterations to convergence 193 setup time was (sec) 0.5600000 now iterating at: 15:04:50 rms-change max change #iterations 3.538555 154.0347 at 10iterations 1.519679 76.07852 at 20iterations 0.6530264 22.87270 at 30iterations 0.2801445 9.924072 at 40iterations 0.1204439 4.168193 at 50iterations 5.1807895E-02 1.965740 at 60iterations 2.2190381E-02 0.8278637 at 70iterations 9.5810508E-03 0.3522625 at 80iterations 4.1249432E-03 0.1561174 at 90iterations 1.7660391E-03 6.2115669E-02 at 100iterations 7.6363573E-04 2.7298927E-02 at 110iterations 3.2799650E-04 1.2056351E-02 at 120iterations finished qdiffx linear iterations at : 15:04:57 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 3.2799650E-04 1.2056351E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 15:04:58 7.789u 0.199s 0:08.27 96.3% 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 Sun Oct 9 2011 at 15:04:58 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2927 !!! WARNING: HIT 110 has a net charge of 0.5140 !!! WARNING: HIT 112 has a net charge of 0.5140 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: 2.535010 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): 0.8360001 49.32900 ymin,ymax (A): -17.14500 31.50400 zmin,zma (A): 124.5990 187.7940 x,y,z range (A): 48.49300 48.64900 63.19501 scale (grids/A): 2.535010 object centre (A): 25.08250 7.179500 156.1965 number of atom coordinates read : 2927 total number of charged atoms : 2786 net assigned charge : 8.528022 assigned positive charge : 440.6283 centred at (gu) : 92.72456 87.97346 86.55183 assigned negative charge : -432.1013 centred at (gu) : 92.72280 88.22422 86.75983 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 159272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27507 grid for indexing accessible points = 1.400000 m= 75353 mr = 112350 m= 23098 mr = 59554 m= 4135 mr = 17519 m= 327 mr = 2779 m= 9 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 358 time to turn everything in is 0.8200000 number of dielectric boundary points 69851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 22275 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) : 1.690007 object centre at (A) : 25.08250 7.179500 156.1965 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1896691 0.1158268 midg,1,midg; midg,igrid,midg 4.3702532E-02 -4.9321286E-02 1,midg,midg; igrid,midg,midg 0.1353443 0.1763046 gauss-seidel spectral radius is 0.9991769 estimated iterations to convergence 275 setup time was (sec) 1.050000 now iterating at: 15:04:59 rms-change max change #iterations 9.018027 271.5067 at 10iterations 5.165802 136.4277 at 20iterations 2.923617 60.20764 at 30iterations 1.655757 35.07275 at 40iterations 0.9291121 20.77018 at 50iterations 0.5221171 10.87598 at 60iterations 0.2920845 6.736710 at 70iterations 0.1634729 3.604476 at 80iterations 9.1442361E-02 1.860901 at 90iterations 5.0991528E-02 0.9701939 at 100iterations 2.8411543E-02 0.5737171 at 110iterations 1.5843300E-02 0.3104343 at 120iterations 8.8336598E-03 0.1792202 at 130iterations 4.9204859E-03 0.1101131 at 140iterations 2.7477515E-03 5.5592537E-02 at 150iterations 1.5270103E-03 3.3256531E-02 at 160iterations 8.5121673E-04 1.6323090E-02 at 170iterations 4.7211786E-04 1.0314941E-02 at 180iterations finished qdiffx linear iterations at : 15:05:10 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 4.7211786E-04 1.0314941E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 15:05:11 12.515u 0.201s 0:13.13 96.8% 0+0k 0+0io 0pf+0w