Mon Oct 10 13:53:20 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 13:53:20 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5714561 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): -11.27100 51.02600 ymin,ymax (A): -12.71500 42.56900 zmin,zma (A): 19.67300 75.95800 x,y,z range (A): 62.29700 55.28400 56.28500 scale (grids/A): 0.5714561 object centre (A): 19.87750 14.92700 47.81550 number of atom coordinates read : 3341 total number of charged atoms : 3184 net assigned charge : 3.030018 assigned positive charge : 517.7900 centred at (gu) : 90.90953 89.83458 87.83266 assigned negative charge : -514.7611 centred at (gu) : 90.82894 89.91819 87.80972 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7369 nv = 96 ne = 84 npr = 64368 no. pairs analyzed = 64368 no. exposed pairs = 4448 no. arc points = 31541 no. surface atoms = 1493 nbur = 1848 mkacc time = 0.1700000 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 = 1.512000 m= 396 mr = 3763 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3068 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9176 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1354528E-11 5.5282784E-10 midg,1,midg; midg,igrid,midg 2.1354909E-09 -1.0800116E-09 1,midg,midg; igrid,midg,midg -8.5276680E-10 2.4834970E-09 gauss-seidel spectral radius is 0.9842359 estimated iterations to convergence 65 setup time was (sec) 0.6700000 now iterating at: 13:53:21 rms-change max change #iterations 9.7199544E-02 13.77621 at 10iterations 7.2059822E-03 1.241905 at 20iterations 5.6425651E-04 8.8396072E-02 at 30iterations 7.2392628E-05 1.0573387E-02 at 40iterations 3.2820768E-05 4.6868324E-03 at 50iterations finished qdiffx linear iterations at : 13:53:25 total time elapsed so far: 4.890000 # loops : 50 mean,max change (kT/e) : 3.2820768E-05 4.6868324E-03 energy calculations done at 4.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.050000 DelPhi exited at 13:53:26 5.059u 0.406s 0:06.12 89.0% 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 13:53:26 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.714368 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): -11.27100 51.02600 ymin,ymax (A): -12.71500 42.56900 zmin,zma (A): 19.67300 75.95800 x,y,z range (A): 62.29700 55.28400 56.28500 scale (grids/A): 1.714368 object centre (A): 19.87750 14.92700 47.81550 number of atom coordinates read : 3341 total number of charged atoms : 3184 net assigned charge : 3.030018 assigned positive charge : 517.7900 centred at (gu) : 92.72773 89.50303 83.49698 assigned negative charge : -514.7611 centred at (gu) : 92.48650 89.75423 83.42877 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31541 grid for indexing accessible points = 1.400000 m= 27305 mr = 54445 m= 3604 mr = 18647 m= 139 mr = 1845 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 36914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 24598 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) : 0.5714561 object centre at (A) : 19.87750 14.92700 47.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2431466E-02 5.2815182E-03 midg,1,midg; midg,igrid,midg 1.7421471E-02 -1.0621094E-02 1,midg,midg; igrid,midg,midg -7.1186093E-03 -9.2414813E-03 gauss-seidel spectral radius is 0.9984035 estimated iterations to convergence 199 setup time was (sec) 0.9600000 now iterating at: 13:53:33 rms-change max change #iterations 4.074149 181.0127 at 10iterations 1.791734 71.77626 at 20iterations 0.7907744 26.96414 at 30iterations 0.3489768 11.93633 at 40iterations 0.1548426 5.201241 at 50iterations 6.8210743E-02 2.244591 at 60iterations 3.0223250E-02 0.9454200 at 70iterations 1.3287014E-02 0.4882362 at 80iterations 5.8715492E-03 0.2056723 at 90iterations 2.6044603E-03 8.5070848E-02 at 100iterations 1.1515960E-03 3.9928943E-02 at 110iterations 5.1431009E-04 1.8429756E-02 at 120iterations finished qdiffx linear iterations at : 13:53:43 total time elapsed so far: 11.36000 # loops : 120 mean,max change (kT/e) : 5.1431009E-04 1.8429756E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 13:53:44 11.528u 0.489s 0:17.92 66.9% 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 13:54:00 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.571552 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): -11.27100 51.02600 ymin,ymax (A): -12.71500 42.56900 zmin,zma (A): 19.67300 75.95800 x,y,z range (A): 62.29700 55.28400 56.28500 scale (grids/A): 2.571552 object centre (A): 19.87750 14.92700 47.81550 number of atom coordinates read : 3341 total number of charged atoms : 3184 net assigned charge : 3.030018 assigned positive charge : 517.7900 centred at (gu) : 94.09139 89.25435 80.24524 assigned negative charge : -514.7611 centred at (gu) : 93.72961 89.63131 80.14300 start vw surface at 0.1400000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 187324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31541 grid for indexing accessible points = 1.400000 m= 90586 mr = 132964 m= 29830 mr = 71396 m= 5971 mr = 22239 m= 612 mr = 4012 m= 12 mr = 318 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 83406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 25435 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) : 1.714368 object centre at (A) : 19.87750 14.92700 47.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2437167 6.5004908E-02 midg,1,midg; midg,igrid,midg 0.2676873 -0.1627164 1,midg,midg; igrid,midg,midg 0.1268482 -0.5702776 gauss-seidel spectral radius is 0.9992175 estimated iterations to convergence 282 setup time was (sec) 2.070000 now iterating at: 13:54:03 rms-change max change #iterations 10.45029 323.6970 at 10iterations 6.156120 138.9077 at 20iterations 3.579712 91.66119 at 30iterations 2.067870 44.93720 at 40iterations 1.189088 25.55330 at 50iterations 0.6809892 15.97054 at 60iterations 0.3904194 8.253937 at 70iterations 0.2227136 4.020211 at 80iterations 0.1267132 2.397143 at 90iterations 7.2180636E-02 1.413841 at 100iterations 4.1055903E-02 0.8021259 at 110iterations 2.3324136E-02 0.4667165 at 120iterations 1.3262055E-02 0.2593040 at 130iterations 7.5349109E-03 0.1515703 at 140iterations 4.2808424E-03 7.9956055E-02 at 150iterations 2.4431243E-03 4.8294067E-02 at 160iterations 1.4072936E-03 2.8047085E-02 at 170iterations 8.2539546E-04 1.5724182E-02 at 180iterations finished qdiffx linear iterations at : 13:54:21 total time elapsed so far: 19.87000 # loops : 180 mean,max change (kT/e) : 8.2539546E-04 1.5724182E-02 energy calculations done at 19.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.03000 DelPhi exited at 13:54:21 20.032u 0.491s 0:21.18 96.8% 0+0k 0+0io 0pf+0w