Tue Oct 11 08:33:36 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 08:33:36 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6619438 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): -10.44700 37.70000 ymin,ymax (A): -25.37300 22.80500 zmin,zma (A): -8.470000 45.31100 x,y,z range (A): 48.14700 48.17800 53.78100 scale (grids/A): 0.6619438 object centre (A): 13.62650 -1.283999 18.42050 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 2.140014 assigned positive charge : 412.8918 centred at (gu) : 89.78948 90.19211 91.26016 assigned negative charge : -410.7524 centred at (gu) : 89.50779 89.99830 91.22082 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8011 nv = 96 ne = 84 npr = 55907 no. pairs analyzed = 55907 no. exposed pairs = 3298 no. arc points = 22958 no. surface atoms = 1110 nbur = 1624 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 4577 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3300000 number of dielectric boundary points 3847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2256 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1449813E-09 1.8749917E-08 midg,1,midg; midg,igrid,midg -3.6162469E-08 4.9493792E-08 1,midg,midg; igrid,midg,midg -6.0661009E-08 6.3046514E-08 gauss-seidel spectral radius is 0.9881800 estimated iterations to convergence 75 setup time was (sec) 0.5800000 now iterating at: 08:33:37 rms-change max change #iterations 0.1753890 22.83911 at 10iterations 1.8764554E-02 2.768293 at 20iterations 2.0264059E-03 0.2445641 at 30iterations 2.2356883E-04 3.0136108E-02 at 40iterations 2.5117995E-05 3.6926270E-03 at 50iterations finished qdiffx linear iterations at : 08:33:41 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 2.5117995E-05 3.6926270E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 08:33:41 4.778u 0.371s 0:05.58 92.1% 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 08:33:41 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.985831 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): -10.44700 37.70000 ymin,ymax (A): -25.37300 22.80500 zmin,zma (A): -8.470000 45.31100 x,y,z range (A): 48.14700 48.17800 53.78100 scale (grids/A): 1.985831 object centre (A): 13.62650 -1.283999 18.42050 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 2.140014 assigned positive charge : 412.8918 centred at (gu) : 89.36790 90.57578 93.77982 assigned negative charge : -410.7524 centred at (gu) : 88.52316 89.99463 93.66226 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 85930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22958 grid for indexing accessible points = 1.400000 m= 32415 mr = 60920 m= 5363 mr = 24201 m= 394 mr = 3437 m= 6 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 540 time to turn everything in is 0.7000000 number of dielectric boundary points 35351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20411 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) : 0.6619438 object centre at (A) : 13.62650 -1.283999 18.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4902755E-02 -4.4693737E-03 midg,1,midg; midg,igrid,midg -2.9660067E-02 3.3491641E-02 1,midg,midg; igrid,midg,midg -1.9682538E-02 7.5733140E-02 gauss-seidel spectral radius is 0.9987538 estimated iterations to convergence 224 setup time was (sec) 1.030000 now iterating at: 08:33:43 rms-change max change #iterations 4.776273 199.6001 at 10iterations 2.317663 69.39636 at 20iterations 1.124657 34.88557 at 30iterations 0.5444260 18.27601 at 40iterations 0.2649118 7.482284 at 50iterations 0.1287979 3.879944 at 60iterations 6.2304821E-02 1.909207 at 70iterations 3.0178785E-02 0.8767891 at 80iterations 1.4736859E-02 0.4431496 at 90iterations 7.1139713E-03 0.2130051 at 100iterations 3.4628997E-03 9.7861290E-02 at 110iterations 1.6863665E-03 5.8422089E-02 at 120iterations finished qdiffx linear iterations at : 08:33:54 total time elapsed so far: 12.11000 # loops : 120 mean,max change (kT/e) : 1.6863665E-03 5.8422089E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 08:33:55 12.276u 0.426s 0:13.25 95.7% 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 08:33:55 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.978747 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): -10.44700 37.70000 ymin,ymax (A): -25.37300 22.80500 zmin,zma (A): -8.470000 45.31100 x,y,z range (A): 48.14700 48.17800 53.78100 scale (grids/A): 2.978747 object centre (A): 13.62650 -1.283999 18.42050 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 2.140014 assigned positive charge : 412.8918 centred at (gu) : 89.05178 90.86343 95.66959 assigned negative charge : -410.7524 centred at (gu) : 87.78465 89.99198 95.49331 start vw surface at 0.1100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 198504 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22958 grid for indexing accessible points = 1.400000 m= 103435 mr = 146855 m= 38952 mr = 85614 m= 9831 mr = 31605 m= 1616 mr = 7544 m= 162 mr = 1166 m= 2 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 1782 time to turn everything in is 1.860000 number of dielectric boundary points 79621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 20651 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) : 1.985831 object centre at (A) : 13.62650 -1.283999 18.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4596365 0.1012049 midg,1,midg; midg,igrid,midg -0.3130590 0.3966426 1,midg,midg; igrid,midg,midg -0.1263311 0.6526599 gauss-seidel spectral radius is 0.9992865 estimated iterations to convergence 295 setup time was (sec) 2.200000 now iterating at: 08:33:58 rms-change max change #iterations 10.88605 413.0634 at 10iterations 6.397674 146.0073 at 20iterations 3.750085 84.36685 at 30iterations 2.198408 45.19995 at 40iterations 1.286464 26.04045 at 50iterations 0.7515404 13.13216 at 60iterations 0.4388314 7.723328 at 70iterations 0.2560127 4.470192 at 80iterations 0.1492075 2.474579 at 90iterations 8.6956792E-02 1.540970 at 100iterations 5.0519086E-02 0.8960619 at 110iterations 2.9452488E-02 0.5124130 at 120iterations 1.7152468E-02 0.2794495 at 130iterations 9.9733053E-03 0.1631145 at 140iterations 5.8213989E-03 9.6541405E-02 at 150iterations 3.3981344E-03 5.6388855E-02 at 160iterations 1.9902531E-03 3.2939911E-02 at 170iterations 1.1712182E-03 1.9813538E-02 at 180iterations finished qdiffx linear iterations at : 08:34:16 total time elapsed so far: 20.48000 # loops : 180 mean,max change (kT/e) : 1.1712182E-03 1.9813538E-02 energy calculations done at 20.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.64000 DelPhi exited at 08:34:16 20.644u 0.490s 0:21.66 97.5% 0+0k 0+0io 0pf+0w