Sat Oct 8 17:03:40 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 Sat Oct 8 2011 at 17:03:40 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4493 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4880122 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): -0.1580000 63.10200 ymin,ymax (A): -30.03900 30.83000 zmin,zma (A): -23.92100 49.02800 x,y,z range (A): 63.26000 60.86900 72.94900 scale (grids/A): 0.4880122 object centre (A): 31.47200 0.3955002 12.55350 number of atom coordinates read : 4493 total number of charged atoms : 4340 net assigned charge : -7.499966 assigned positive charge : 688.0413 centred at (gu) : 90.66238 91.16804 90.38123 assigned negative charge : -695.5461 centred at (gu) : 90.71841 91.14958 90.41743 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6873 nv = 96 ne = 84 npr = 87281 no. pairs analyzed = 87281 no. exposed pairs = 6009 no. arc points = 42845 no. surface atoms = 2000 nbur = 2493 mkacc time = 0.1900000 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 = 1.764000 m= 257 mr = 3306 m= 0 mr = 10 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4133 ## 742 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9339 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4482825E-12 -7.7858060E-11 midg,1,midg; midg,igrid,midg -3.9241367E-11 -2.6841489E-11 1,midg,midg; igrid,midg,midg 1.1658540E-11 -1.0630564E-10 gauss-seidel spectral radius is 0.9785324 estimated iterations to convergence 57 setup time was (sec) 0.6200000 now iterating at: 17:03:41 rms-change max change #iterations 5.1292848E-02 9.252487 at 10iterations 2.6285769E-03 0.4408150 at 20iterations 2.8837478E-04 6.5226555E-02 at 30iterations 7.1676710E-05 1.8335342E-02 at 40iterations 1.9985664E-05 5.1651001E-03 at 50iterations finished qdiffx linear iterations at : 17:03:44 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.9985664E-05 5.1651001E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 17:03:44 3.230u 0.131s 0:03.66 91.8% 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 Sat Oct 8 2011 at 17:03:44 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4493 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: 1.464037 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): -0.1580000 63.10200 ymin,ymax (A): -30.03900 30.83000 zmin,zma (A): -23.92100 49.02800 x,y,z range (A): 63.26000 60.86900 72.94900 scale (grids/A): 1.464037 object centre (A): 31.47200 0.3955002 12.55350 number of atom coordinates read : 4493 total number of charged atoms : 4340 net assigned charge : -7.499966 assigned positive charge : 688.0413 centred at (gu) : 91.98579 93.50223 91.14230 assigned negative charge : -695.5461 centred at (gu) : 92.15469 93.44856 91.25202 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42845 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 20803 mr = 50984 m= 1512 mr = 13076 m= 33 mr = 544 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 824 time to turn everything in is 0.5300000 number of dielectric boundary points 35791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 678 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 32053 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) : 0.4880122 object centre at (A) : 31.47200 0.3955002 12.55350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0033866E-03 -1.3366467E-02 midg,1,midg; midg,igrid,midg -8.8743223E-03 -5.1829824E-03 1,midg,midg; igrid,midg,midg 4.9288110E-03 -1.1763213E-03 gauss-seidel spectral radius is 0.9978901 estimated iterations to convergence 173 setup time was (sec) 0.7900000 now iterating at: 17:03:45 rms-change max change #iterations 3.318940 158.7288 at 10iterations 1.292193 45.30154 at 20iterations 0.5003470 20.35593 at 30iterations 0.1954678 6.711959 at 40iterations 7.6310426E-02 2.598763 at 50iterations 2.9660054E-02 0.9925728 at 60iterations 1.1518959E-02 0.3905892 at 70iterations 4.5273304E-03 0.1752357 at 80iterations 1.7828662E-03 5.9820175E-02 at 90iterations 7.0563174E-04 2.7334690E-02 at 100iterations 2.8916824E-04 1.1358261E-02 at 110iterations 1.2450737E-04 4.7092438E-03 at 120iterations finished qdiffx linear iterations at : 17:03:51 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.2450737E-04 4.7092438E-03 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 17:03:52 6.966u 0.145s 0:07.41 95.8% 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 Sat Oct 8 2011 at 17:03:52 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4493 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.196055 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): -0.1580000 63.10200 ymin,ymax (A): -30.03900 30.83000 zmin,zma (A): -23.92100 49.02800 x,y,z range (A): 63.26000 60.86900 72.94900 scale (grids/A): 2.196055 object centre (A): 31.47200 0.3955002 12.55350 number of atom coordinates read : 4493 total number of charged atoms : 4340 net assigned charge : -7.499966 assigned positive charge : 688.0413 centred at (gu) : 92.97809 95.25313 91.71307 assigned negative charge : -695.5461 centred at (gu) : 93.23189 95.17271 91.87795 start vw surface at 0.1900000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 181616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42845 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 76997 mr = 125856 m= 17317 mr = 58374 m= 1939 mr = 11823 m= 62 mr = 996 m= 0 mr = 9 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 3014 time to turn everything in is 1.260000 number of dielectric boundary points 80873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 34536 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) : 1.464037 object centre at (A) : 31.47200 0.3955002 12.55350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1601934 -0.1549971 midg,1,midg; midg,igrid,midg -0.2610110 -8.6519375E-02 1,midg,midg; igrid,midg,midg 6.1699290E-02 -4.5625538E-02 gauss-seidel spectral radius is 0.9990820 estimated iterations to convergence 261 setup time was (sec) 1.550000 now iterating at: 17:03:53 rms-change max change #iterations 9.368892 340.2328 at 10iterations 5.245080 141.4437 at 20iterations 2.908306 68.13326 at 30iterations 1.607493 38.49993 at 40iterations 0.8800508 21.26695 at 50iterations 0.4829131 10.73606 at 60iterations 0.2633079 6.413834 at 70iterations 0.1431705 3.094620 at 80iterations 7.7794507E-02 1.757428 at 90iterations 4.2097278E-02 0.9420319 at 100iterations 2.2860693E-02 0.4544830 at 110iterations 1.2393932E-02 0.2577267 at 120iterations 6.7405342E-03 0.1345673 at 130iterations 3.6530285E-03 7.1010590E-02 at 140iterations 1.9873953E-03 3.8822174E-02 at 150iterations 1.0890530E-03 2.4108887E-02 at 160iterations 6.0106895E-04 1.2512207E-02 at 170iterations 3.3616452E-04 7.1690083E-03 at 180iterations finished qdiffx linear iterations at : 17:04:03 total time elapsed so far: 11.08000 # loops : 180 mean,max change (kT/e) : 3.3616452E-04 7.1690083E-03 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 17:04:03 11.253u 0.165s 0:11.71 97.4% 0+0k 0+0io 0pf+0w