Mon Oct 10 22:53:19 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 22:53:19 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6496113 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): -8.420000 46.38200 ymin,ymax (A): -15.29400 29.97000 zmin,zma (A): -11.48600 41.94600 x,y,z range (A): 54.80200 45.26400 53.43200 scale (grids/A): 0.6496113 object centre (A): 18.98100 7.338001 15.23000 number of atom coordinates read : 2680 total number of charged atoms : 2528 net assigned charge : 2.312014 assigned positive charge : 403.8106 centred at (gu) : 89.45814 90.09519 89.04990 assigned negative charge : -401.4994 centred at (gu) : 89.74635 90.05082 89.05640 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7585 nv = 96 ne = 84 npr = 54606 no. pairs analyzed = 54606 no. exposed pairs = 3222 no. arc points = 22462 no. surface atoms = 1098 nbur = 1582 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 4312 m= 0 mr = 48 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.4200000 number of dielectric boundary points 3649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2115 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3407746E-09 2.6339479E-09 midg,1,midg; midg,igrid,midg -2.7043947E-09 1.1314639E-08 1,midg,midg; igrid,midg,midg 5.3726151E-08 -3.7556564E-08 gauss-seidel spectral radius is 0.9877265 estimated iterations to convergence 74 setup time was (sec) 0.7200000 now iterating at: 22:53:20 rms-change max change #iterations 0.1579513 21.65612 at 10iterations 1.7344316E-02 2.322903 at 20iterations 2.4762789E-03 0.4354134 at 30iterations 6.2088604E-04 0.1299782 at 40iterations 1.9101753E-04 4.0496826E-02 at 50iterations finished qdiffx linear iterations at : 22:53:23 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 1.9101753E-04 4.0496826E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 22:53:24 4.369u 0.228s 0:05.20 88.0% 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 22:53:24 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.948834 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): -8.420000 46.38200 ymin,ymax (A): -15.29400 29.97000 zmin,zma (A): -11.48600 41.94600 x,y,z range (A): 54.80200 45.26400 53.43200 scale (grids/A): 1.948834 object centre (A): 18.98100 7.338001 15.23000 number of atom coordinates read : 2680 total number of charged atoms : 2528 net assigned charge : 2.312014 assigned positive charge : 403.8106 centred at (gu) : 88.37395 90.28498 87.14918 assigned negative charge : -401.4994 centred at (gu) : 89.23884 90.15223 87.16888 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 81789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22462 grid for indexing accessible points = 1.400000 m= 30163 mr = 57406 m= 4879 mr = 22861 m= 270 mr = 3167 m= 2 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 969 time to turn everything in is 0.7600000 number of dielectric boundary points 33558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 19962 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) : 0.6496113 object centre at (A) : 18.98100 7.338001 15.23000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9419772E-02 6.0318159E-03 midg,1,midg; midg,igrid,midg 1.8442821E-02 1.8324718E-02 1,midg,midg; igrid,midg,midg 5.6655794E-02 -6.6764288E-02 gauss-seidel spectral radius is 0.9986992 estimated iterations to convergence 220 setup time was (sec) 1.130000 now iterating at: 22:53:26 rms-change max change #iterations 4.542319 176.8096 at 10iterations 2.167193 75.26765 at 20iterations 1.033538 30.81344 at 30iterations 0.4907524 15.23907 at 40iterations 0.2345630 7.599835 at 50iterations 0.1124650 3.444079 at 60iterations 5.3725727E-02 1.663072 at 70iterations 2.5722068E-02 0.7489052 at 80iterations 1.2438499E-02 0.3678513 at 90iterations 6.1064796E-03 0.1790504 at 100iterations 3.0519806E-03 9.7377777E-02 at 110iterations 1.5982779E-03 5.7567596E-02 at 120iterations finished qdiffx linear iterations at : 22:53:34 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 1.5982779E-03 5.7567596E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 22:53:35 9.700u 0.263s 0:10.51 94.7% 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 22:53:35 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.923251 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): -8.420000 46.38200 ymin,ymax (A): -15.29400 29.97000 zmin,zma (A): -11.48600 41.94600 x,y,z range (A): 54.80200 45.26400 53.43200 scale (grids/A): 2.923251 object centre (A): 18.98100 7.338001 15.23000 number of atom coordinates read : 2680 total number of charged atoms : 2528 net assigned charge : 2.312014 assigned positive charge : 403.8106 centred at (gu) : 87.56078 90.42709 85.72358 assigned negative charge : -401.4994 centred at (gu) : 88.85822 90.22820 85.75317 start vw surface at 0.1900000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 188836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22462 grid for indexing accessible points = 1.400000 m= 97295 mr = 138698 m= 36068 mr = 80739 m= 8892 mr = 29494 m= 1402 mr = 6923 m= 89 mr = 981 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 3344 time to turn everything in is 1.930000 number of dielectric boundary points 75695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 20224 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) : 1.948834 object centre at (A) : 18.98100 7.338001 15.23000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3452961 -4.1802522E-02 midg,1,midg; midg,igrid,midg 0.2749399 0.1831019 1,midg,midg; igrid,midg,midg 0.6888397 -0.6650663 gauss-seidel spectral radius is 0.9992705 estimated iterations to convergence 292 setup time was (sec) 2.330000 now iterating at: 22:53:38 rms-change max change #iterations 10.45905 423.3619 at 10iterations 6.100922 126.5259 at 20iterations 3.548442 78.91487 at 30iterations 2.054231 37.20428 at 40iterations 1.191864 24.22613 at 50iterations 0.6897502 13.62817 at 60iterations 0.3991548 7.027832 at 70iterations 0.2305453 3.979648 at 80iterations 0.1331184 2.391331 at 90iterations 7.7131420E-02 1.238439 at 100iterations 4.4479318E-02 0.8215790 at 110iterations 2.5828192E-02 0.4854450 at 120iterations 1.4971764E-02 0.2546539 at 130iterations 8.7528173E-03 0.1521912 at 140iterations 5.1709763E-03 8.6753845E-02 at 150iterations 3.1244766E-03 6.7695618E-02 at 160iterations 1.9384056E-03 4.5307159E-02 at 170iterations 1.2663439E-03 3.0097961E-02 at 180iterations finished qdiffx linear iterations at : 22:53:51 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 1.2663439E-03 3.0097961E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.65000 DelPhi exited at 22:53:52 15.650u 0.272s 0:16.68 95.4% 0+0k 0+0io 0pf+0w