Sun Oct 9 09:41:08 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 Sun Oct 9 2011 at 09:41:08 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 = 2571 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: 0.6082455 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 0.6082455 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.5930 centred at (gu) : 88.80954 89.82970 89.55660 assigned negative charge : -368.5935 centred at (gu) : 88.76950 89.91656 89.48371 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6467 nv = 96 ne = 84 npr = 51548 no. pairs analyzed = 51548 no. exposed pairs = 3328 no. arc points = 23846 no. surface atoms = 1114 nbur = 1457 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 302 mr = 3316 m= 3 mr = 26 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 3430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2442 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0094792E-10 5.9819034E-09 midg,1,midg; midg,igrid,midg 7.4904465E-09 -4.9801296E-10 1,midg,midg; igrid,midg,midg 2.0298188E-09 3.9718464E-09 gauss-seidel spectral radius is 0.9860137 estimated iterations to convergence 69 setup time was (sec) 0.5300000 now iterating at: 09:41:08 rms-change max change #iterations 0.1118917 18.00717 at 10iterations 9.9265007E-03 1.912704 at 20iterations 8.7121705E-04 0.1394424 at 30iterations 7.6639095E-05 1.1781693E-02 at 40iterations 6.8580280E-06 1.0643005E-03 at 50iterations finished qdiffx linear iterations at : 09:41:11 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 6.8580280E-06 1.0643005E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 09:41:12 3.272u 0.179s 0:03.77 91.2% 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 09:41:12 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 = 2571 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: 1.824736 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 1.824736 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.5930 centred at (gu) : 86.42809 89.48877 88.66938 assigned negative charge : -368.5935 centred at (gu) : 86.30804 89.74954 88.45090 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23846 grid for indexing accessible points = 1.400000 m= 24012 mr = 47029 m= 3358 mr = 16955 m= 175 mr = 1758 m= 0 mr = 47 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 31806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19019 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) : 0.6082455 object centre at (A) : 20.57050 42.06400 91.99850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8409504E-02 1.2913952E-02 midg,1,midg; midg,igrid,midg 3.3520479E-02 1.3468516E-03 1,midg,midg; igrid,midg,midg -1.5009348E-02 1.5308146E-02 gauss-seidel spectral radius is 0.9985256 estimated iterations to convergence 207 setup time was (sec) 0.8000000 now iterating at: 09:41:13 rms-change max change #iterations 3.806865 170.8312 at 10iterations 1.729067 65.73030 at 20iterations 0.7825149 27.81553 at 30iterations 0.3557799 11.95519 at 40iterations 0.1609418 5.127504 at 50iterations 7.3174953E-02 2.561291 at 60iterations 3.3283163E-02 1.082364 at 70iterations 1.5038737E-02 0.5707233 at 80iterations 6.8649207E-03 0.2556944 at 90iterations 3.1097315E-03 0.1004028 at 100iterations 1.4109978E-03 4.6468377E-02 at 110iterations 6.4105797E-04 2.1772385E-02 at 120iterations finished qdiffx linear iterations at : 09:41:19 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 6.4105797E-04 2.1772385E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 09:41:19 7.382u 0.206s 0:07.85 96.5% 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 09:41:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 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: 2.737105 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 2.737105 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.5930 centred at (gu) : 84.64206 89.23297 88.00397 assigned negative charge : -368.5935 centred at (gu) : 84.46202 89.62418 87.67628 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 162141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23846 grid for indexing accessible points = 1.400000 m= 78458 mr = 114777 m= 26633 mr = 62357 m= 5559 mr = 20491 m= 706 mr = 3744 m= 21 mr = 411 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 71736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 19439 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) : 1.824736 object centre at (A) : 20.57050 42.06400 91.99850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4798144 3.9925717E-02 midg,1,midg; midg,igrid,midg 0.3274027 -2.3787923E-02 1,midg,midg; igrid,midg,midg -0.2809847 0.1521681 gauss-seidel spectral radius is 0.9992350 estimated iterations to convergence 285 setup time was (sec) 1.540000 now iterating at: 09:41:21 rms-change max change #iterations 9.265481 327.0555 at 10iterations 5.433546 138.8872 at 20iterations 3.146670 75.88541 at 30iterations 1.815414 42.20675 at 40iterations 1.045179 20.80959 at 50iterations 0.5986496 13.45539 at 60iterations 0.3425889 7.288910 at 70iterations 0.1958452 4.238152 at 80iterations 0.1118734 2.270749 at 90iterations 6.3751563E-02 1.272351 at 100iterations 3.6429174E-02 0.7367630 at 110iterations 2.0702504E-02 0.3985615 at 120iterations 1.1804051E-02 0.2246685 at 130iterations 6.7181946E-03 0.1399078 at 140iterations 3.8228722E-03 8.4877014E-02 at 150iterations 2.1752547E-03 4.6452045E-02 at 160iterations 1.2411887E-03 2.4782181E-02 at 170iterations 7.0766045E-04 1.2725830E-02 at 180iterations finished qdiffx linear iterations at : 09:41:32 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 7.0766045E-04 1.2725830E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 09:41:32 12.080u 0.209s 0:12.60 97.4% 0+0k 0+0io 0pf+0w