Tue Oct 11 08:00:48 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 Tue Oct 11 2011 at 08:00:48 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5426415 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): -17.28600 27.87300 ymin,ymax (A): -3.805000 52.75100 zmin,zma (A): 7.289999 72.89500 x,y,z range (A): 45.15900 56.55600 65.60500 scale (grids/A): 0.5426415 object centre (A): 5.293500 24.47300 40.09250 number of atom coordinates read : 2517 total number of charged atoms : 2376 net assigned charge : 11.00002 assigned positive charge : 373.2076 centred at (gu) : 88.80875 90.34481 91.90551 assigned negative charge : -362.2085 centred at (gu) : 88.74000 90.30911 91.71735 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4870 nv = 96 ne = 84 npr = 48893 no. pairs analyzed = 48893 no. exposed pairs = 3390 no. arc points = 24336 no. surface atoms = 1135 nbur = 1382 mkacc time = 9.0000004E-02 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 = 1.568000 m= 192 mr = 2307 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2491 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6322 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9795773E-10 2.3482669E-09 midg,1,midg; midg,igrid,midg 3.8002329E-10 8.1730872E-10 1,midg,midg; igrid,midg,midg 3.3157571E-10 6.7783784E-10 gauss-seidel spectral radius is 0.9824666 estimated iterations to convergence 62 setup time was (sec) 0.3700000 now iterating at: 08:00:48 rms-change max change #iterations 6.4169496E-02 11.77147 at 10iterations 4.0506856E-03 0.7485275 at 20iterations 2.6511843E-04 5.3642273E-02 at 30iterations 1.7669759E-05 3.9930344E-03 at 40iterations 1.1831751E-06 2.2888184E-04 at 50iterations finished qdiffx linear iterations at : 08:00:51 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1831751E-06 2.2888184E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:00:51 3.351u 0.175s 0:03.81 92.3% 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 Tue Oct 11 2011 at 08:00:51 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.627925 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): -17.28600 27.87300 ymin,ymax (A): -3.805000 52.75100 zmin,zma (A): 7.289999 72.89500 x,y,z range (A): 45.15900 56.55600 65.60500 scale (grids/A): 1.627925 object centre (A): 5.293500 24.47300 40.09250 number of atom coordinates read : 2517 total number of charged atoms : 2376 net assigned charge : 11.00002 assigned positive charge : 373.2076 centred at (gu) : 86.42552 91.03369 95.71600 assigned negative charge : -362.2085 centred at (gu) : 86.21975 90.92708 95.15163 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 54138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24336 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15028 mr = 34593 m= 1402 mr = 9747 m= 39 mr = 647 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 207 time to turn everything in is 0.2700000 number of dielectric boundary points 25620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 18151 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) : 0.5426415 object centre at (A) : 5.293500 24.47300 40.09250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4121533E-02 5.8764566E-02 midg,1,midg; midg,igrid,midg 5.3965915E-03 6.5836213E-03 1,midg,midg; igrid,midg,midg 6.7782584E-03 7.4849292E-03 gauss-seidel spectral radius is 0.9981270 estimated iterations to convergence 184 setup time was (sec) 0.4800000 now iterating at: 08:00:52 rms-change max change #iterations 2.946245 153.9157 at 10iterations 1.204893 57.44992 at 20iterations 0.4925533 19.39991 at 30iterations 0.2017715 8.338860 at 40iterations 8.2350299E-02 3.317039 at 50iterations 3.3999864E-02 1.316086 at 60iterations 1.3936719E-02 0.6146507 at 70iterations 5.7008741E-03 0.2241316 at 80iterations 2.3554296E-03 9.8660469E-02 at 90iterations 9.6271047E-04 4.4994354E-02 at 100iterations 3.9466858E-04 1.6235352E-02 at 110iterations 1.6305955E-04 6.6804886E-03 at 120iterations finished qdiffx linear iterations at : 08:00:59 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.6305955E-04 6.6804886E-03 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 08:01:00 7.590u 0.197s 0:08.51 91.4% 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 Tue Oct 11 2011 at 08:01:00 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.441887 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): -17.28600 27.87300 ymin,ymax (A): -3.805000 52.75100 zmin,zma (A): 7.289999 72.89500 x,y,z range (A): 45.15900 56.55600 65.60500 scale (grids/A): 2.441887 object centre (A): 5.293500 24.47300 40.09250 number of atom coordinates read : 2517 total number of charged atoms : 2376 net assigned charge : 11.00002 assigned positive charge : 373.2076 centred at (gu) : 84.63804 91.55048 98.57373 assigned negative charge : -362.2085 centred at (gu) : 84.32945 91.39056 97.72742 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 125749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24336 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 53176 mr = 85296 m= 13784 mr = 40803 m= 2074 mr = 9701 m= 127 mr = 1258 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 751 time to turn everything in is 0.6400000 number of dielectric boundary points 57813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 18981 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) : 1.627925 object centre at (A) : 5.293500 24.47300 40.09250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1228577 1.226444 midg,1,midg; midg,igrid,midg 5.6820836E-02 4.8571028E-02 1,midg,midg; igrid,midg,midg 8.7946951E-02 9.8209113E-02 gauss-seidel spectral radius is 0.9991075 estimated iterations to convergence 264 setup time was (sec) 0.8700000 now iterating at: 08:01:01 rms-change max change #iterations 7.649806 288.0201 at 10iterations 4.230706 123.9259 at 20iterations 2.323133 59.05289 at 30iterations 1.271496 29.66629 at 40iterations 0.6965781 15.80702 at 50iterations 0.3785723 8.896592 at 60iterations 0.2059548 4.616817 at 70iterations 0.1119385 2.410353 at 80iterations 6.0717810E-02 1.309416 at 90iterations 3.3010468E-02 0.7225249 at 100iterations 1.7925918E-02 0.4579034 at 110iterations 9.7202212E-03 0.2166481 at 120iterations 5.2778325E-03 0.1155338 at 130iterations 2.8605917E-03 6.1218262E-02 at 140iterations 1.5536644E-03 3.4221649E-02 at 150iterations 8.4346201E-04 1.7871380E-02 at 160iterations 4.5693613E-04 1.1260986E-02 at 170iterations 2.4797092E-04 5.6209564E-03 at 180iterations finished qdiffx linear iterations at : 08:01:12 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 2.4797092E-04 5.6209564E-03 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 08:01:13 12.004u 0.198s 0:12.48 97.6% 0+0k 0+0io 0pf+0w