Sun Oct 9 13:58:51 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 13:58:51 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 0.6907525 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): -6.965000 44.57300 ymin,ymax (A): 22.01400 73.26300 zmin,zma (A): 42.00100 84.90500 x,y,z range (A): 51.53800 51.24900 42.90400 scale (grids/A): 0.6907525 object centre (A): 18.80400 47.63850 63.45300 number of atom coordinates read : 2392 total number of charged atoms : 2251 net assigned charge : 4.500021 assigned positive charge : 367.2191 centred at (gu) : 89.82590 91.25243 90.34037 assigned negative charge : -362.7196 centred at (gu) : 89.82329 91.41949 90.41723 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7711 nv = 96 ne = 84 npr = 47797 no. pairs analyzed = 47797 no. exposed pairs = 3052 no. arc points = 21378 no. surface atoms = 1018 nbur = 1374 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4207 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2018 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8738 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2640146E-08 -4.3213237E-09 midg,1,midg; midg,igrid,midg 7.0763726E-08 -5.2481919E-08 1,midg,midg; igrid,midg,midg 2.6268790E-08 2.6547971E-08 gauss-seidel spectral radius is 0.9891135 estimated iterations to convergence 78 setup time was (sec) 0.5100000 now iterating at: 13:58:52 rms-change max change #iterations 0.1955158 25.51192 at 10iterations 2.3203909E-02 3.032337 at 20iterations 3.1524491E-03 0.4982872 at 30iterations 6.8692619E-04 0.1151428 at 40iterations 2.2433612E-04 3.9768219E-02 at 50iterations finished qdiffx linear iterations at : 13:58:54 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 2.2433612E-04 3.9768219E-02 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 13:58:55 3.239u 0.179s 0:03.68 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 Sun Oct 9 2011 at 13:58:55 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 2.072258 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): -6.965000 44.57300 ymin,ymax (A): 22.01400 73.26300 zmin,zma (A): 42.00100 84.90500 x,y,z range (A): 51.53800 51.24900 42.90400 scale (grids/A): 2.072258 object centre (A): 18.80400 47.63850 63.45300 number of atom coordinates read : 2392 total number of charged atoms : 2251 net assigned charge : 4.500021 assigned positive charge : 367.2191 centred at (gu) : 89.47720 93.75719 91.02061 assigned negative charge : -362.7196 centred at (gu) : 89.46955 94.25819 91.25153 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21378 grid for indexing accessible points = 1.400000 m= 31434 mr = 56647 m= 5730 mr = 23372 m= 569 mr = 3719 m= 17 mr = 336 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 264 time to turn everything in is 0.6100000 number of dielectric boundary points 35532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17859 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) : 0.6907525 object centre at (A) : 18.80400 47.63850 63.45300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2533461E-02 -1.4589695E-03 midg,1,midg; midg,igrid,midg 1.9010980E-02 -4.6403568E-02 1,midg,midg; igrid,midg,midg 5.9584141E-02 8.7550906E-03 gauss-seidel spectral radius is 0.9988209 estimated iterations to convergence 231 setup time was (sec) 0.8800000 now iterating at: 13:58:56 rms-change max change #iterations 4.875152 242.1954 at 10iterations 2.397729 75.16846 at 20iterations 1.186908 38.16565 at 30iterations 0.5865928 18.50846 at 40iterations 0.2893128 9.776672 at 50iterations 0.1438403 4.003368 at 60iterations 7.1145914E-02 2.184965 at 70iterations 3.5215586E-02 1.186440 at 80iterations 1.7585358E-02 0.5455513 at 90iterations 8.8108536E-03 0.2701941 at 100iterations 4.4971453E-03 0.1331787 at 110iterations 2.3705144E-03 8.2105637E-02 at 120iterations finished qdiffx linear iterations at : 13:59:02 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 2.3705144E-03 8.2105637E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 13:59:03 7.439u 0.192s 0:07.90 96.4% 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 Sun Oct 9 2011 at 13:59:03 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 3.108386 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): -6.965000 44.57300 ymin,ymax (A): 22.01400 73.26300 zmin,zma (A): 42.00100 84.90500 x,y,z range (A): 51.53800 51.24900 42.90400 scale (grids/A): 3.108386 object centre (A): 18.80400 47.63850 63.45300 number of atom coordinates read : 2392 total number of charged atoms : 2251 net assigned charge : 4.500021 assigned positive charge : 367.2191 centred at (gu) : 89.21570 95.63548 91.53085 assigned negative charge : -362.7196 centred at (gu) : 89.20427 96.38715 91.87724 start vw surface at 0.1400000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 188802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21378 grid for indexing accessible points = 1.400000 m= 98614 mr = 136844 m= 38866 mr = 80768 m= 10737 mr = 31769 m= 2248 mr = 8183 m= 342 mr = 1723 m= 8 mr = 245 m= 0 mr = 0 time to grow re-entrant surface = 0.8999999 no. cavity mid-points inaccessible to solvent = 875 time to turn everything in is 1.840000 number of dielectric boundary points 80085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 18003 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) : 2.072258 object centre at (A) : 18.80400 47.63850 63.45300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6151796 -0.1078398 midg,1,midg; midg,igrid,midg 0.2624330 -0.5704468 1,midg,midg; igrid,midg,midg 0.7013211 -0.1974215 gauss-seidel spectral radius is 0.9992996 estimated iterations to convergence 298 setup time was (sec) 2.140000 now iterating at: 13:59:05 rms-change max change #iterations 10.93702 358.5469 at 10iterations 6.472797 135.5419 at 20iterations 3.820200 68.14465 at 30iterations 2.254107 46.17487 at 40iterations 1.330498 22.83591 at 50iterations 0.7814866 13.99091 at 60iterations 0.4585452 7.257901 at 70iterations 0.2688837 4.367775 at 80iterations 0.1577917 2.644676 at 90iterations 9.2563495E-02 1.576706 at 100iterations 5.4359928E-02 1.093602 at 110iterations 3.2045782E-02 0.5667267 at 120iterations 1.8998416E-02 0.3144206 at 130iterations 1.1446490E-02 0.2267284 at 140iterations 7.0789941E-03 0.1305199 at 150iterations 4.5736004E-03 9.6969604E-02 at 160iterations 3.1097722E-03 6.5509796E-02 at 170iterations 2.2634976E-03 5.0868988E-02 at 180iterations finished qdiffx linear iterations at : 13:59:17 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 2.2634976E-03 5.0868988E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 13:59:17 13.805u 0.214s 0:14.28 98.1% 0+0k 0+0io 0pf+0w