Tue Oct 11 05:59:54 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+sph.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 = amb.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 05:59:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 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: 0.7608789 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): -18.02600 28.76200 ymin,ymax (A): -11.74500 30.71900 zmin,zma (A): -8.487000 38.07900 x,y,z range (A): 46.78800 42.46400 46.56600 scale (grids/A): 0.7608789 object centre (A): 5.368000 9.487000 14.79600 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 7.500009 assigned positive charge : 312.6270 centred at (gu) : 90.55734 89.86254 90.97318 assigned negative charge : -305.1272 centred at (gu) : 90.43320 89.78987 90.84370 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8320 nv = 96 ne = 84 npr = 41344 no. pairs analyzed = 41344 no. exposed pairs = 2518 no. arc points = 17237 no. surface atoms = 854 nbur = 1207 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 624 mr = 4944 m= 6 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1800000 number of dielectric boundary points 3870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1441 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8590 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0664179E-08 4.6540430E-07 midg,1,midg; midg,igrid,midg 9.7346572E-08 3.0062930E-07 1,midg,midg; igrid,midg,midg 1.7827970E-08 4.2284262E-07 gauss-seidel spectral radius is 0.9909848 estimated iterations to convergence 85 setup time was (sec) 0.3700000 now iterating at: 05:59:55 rms-change max change #iterations 0.2663079 39.77019 at 10iterations 3.8398597E-02 4.860821 at 20iterations 5.5972575E-03 0.7128906 at 30iterations 8.7915693E-04 0.1103897 at 40iterations 1.8870202E-04 2.3902893E-02 at 50iterations finished qdiffx linear iterations at : 05:59:58 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.8870202E-04 2.3902893E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 05:59:58 3.366u 0.176s 0:04.20 84.0% 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 Tue Oct 11 2011 at 05:59:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 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: 2.282637 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): -18.02600 28.76200 ymin,ymax (A): -11.74500 30.71900 zmin,zma (A): -8.487000 38.07900 x,y,z range (A): 46.78800 42.46400 46.56600 scale (grids/A): 2.282637 object centre (A): 5.368000 9.487000 14.79600 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 7.500009 assigned positive charge : 312.6270 centred at (gu) : 91.67219 89.58776 92.91953 assigned negative charge : -305.1272 centred at (gu) : 91.29965 89.36978 92.53126 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17237 grid for indexing accessible points = 1.400000 m= 38069 mr = 62307 m= 8668 mr = 29698 m= 1030 mr = 6120 m= 48 mr = 605 m= 0 mr = 7 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 201 time to turn everything in is 0.4600000 number of dielectric boundary points 35860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 15414 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) : 0.7608789 object centre at (A) : 5.368000 9.487000 14.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6697968E-02 5.6292310E-02 midg,1,midg; midg,igrid,midg 3.7939589E-02 3.5564411E-02 1,midg,midg; igrid,midg,midg 5.3710159E-02 0.1217075 gauss-seidel spectral radius is 0.9989642 estimated iterations to convergence 246 setup time was (sec) 0.6800000 now iterating at: 05:59:59 rms-change max change #iterations 5.189939 222.7511 at 10iterations 2.694508 84.15537 at 20iterations 1.387276 44.87108 at 30iterations 0.7191174 18.91371 at 40iterations 0.3717559 9.918884 at 50iterations 0.1918408 5.644045 at 60iterations 9.9459402E-02 2.543166 at 70iterations 5.1461343E-02 1.522064 at 80iterations 2.6716359E-02 0.6826944 at 90iterations 1.3902890E-02 0.3926373 at 100iterations 7.2526531E-03 0.1987906 at 110iterations 3.8155976E-03 0.1074457 at 120iterations finished qdiffx linear iterations at : 06:00:06 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 3.8155976E-03 0.1074457 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 06:00:07 8.014u 0.193s 0:08.55 95.9% 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 Tue Oct 11 2011 at 06:00:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.423955 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): -18.02600 28.76200 ymin,ymax (A): -11.74500 30.71900 zmin,zma (A): -8.487000 38.07900 x,y,z range (A): 46.78800 42.46400 46.56600 scale (grids/A): 3.423955 object centre (A): 5.368000 9.487000 14.79600 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 7.500009 assigned positive charge : 312.6270 centred at (gu) : 92.50829 89.38174 94.37924 assigned negative charge : -305.1272 centred at (gu) : 91.94949 89.05472 93.79689 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 199168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17237 grid for indexing accessible points = 1.400000 m= 114378 mr = 149026 m= 51822 mr = 96516 m= 17113 mr = 43683 m= 4134 mr = 13720 m= 673 mr = 3187 m= 55 mr = 469 m= 5 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.380000 number of dielectric boundary points 80724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 15464 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) : 2.282637 object centre at (A) : 5.368000 9.487000 14.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6204338 0.4814898 midg,1,midg; midg,igrid,midg 0.3043309 0.1471537 1,midg,midg; igrid,midg,midg 0.3217265 0.8029528 gauss-seidel spectral radius is 0.9993317 estimated iterations to convergence 305 setup time was (sec) 1.620000 now iterating at: 06:00:09 rms-change max change #iterations 11.20790 260.4223 at 10iterations 6.771202 150.8294 at 20iterations 4.064209 80.80147 at 30iterations 2.431715 44.19348 at 40iterations 1.452236 31.36564 at 50iterations 0.8698602 15.09467 at 60iterations 0.5173077 8.655722 at 70iterations 0.3081016 5.137508 at 80iterations 0.1836318 3.457211 at 90iterations 0.1092166 1.842303 at 100iterations 6.4898036E-02 1.085764 at 110iterations 3.8793184E-02 0.6667194 at 120iterations 2.3216097E-02 0.3902912 at 130iterations 1.4052385E-02 0.2348156 at 140iterations 8.6599560E-03 0.1398983 at 150iterations 5.4949289E-03 9.2674255E-02 at 160iterations 3.6445870E-03 6.0638428E-02 at 170iterations 2.5637727E-03 4.7233582E-02 at 180iterations finished qdiffx linear iterations at : 06:00:20 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 2.5637727E-03 4.7233582E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 06:00:21 13.091u 0.221s 0:13.75 96.8% 0+0k 0+0io 0pf+0w