Sat Oct 8 22:15:07 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 Sat Oct 8 2011 at 22:15:07 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2242 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6506561 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): -14.77600 27.69600 ymin,ymax (A): -11.92900 42.12100 zmin,zma (A): -4.6999931E-02 54.66700 x,y,z range (A): 42.47200 54.05000 54.71400 scale (grids/A): 0.6506561 object centre (A): 6.460001 15.09600 27.31000 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 11.51402 assigned positive charge : 328.2416 centred at (gu) : 88.48225 91.20869 89.22999 assigned negative charge : -316.7282 centred at (gu) : 88.55864 91.22585 89.23738 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6562 nv = 96 ne = 84 npr = 44300 no. pairs analyzed = 44300 no. exposed pairs = 3069 no. arc points = 21416 no. surface atoms = 1027 nbur = 1215 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3399 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2700000 number of dielectric boundary points 3538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2036 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7640 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7326733E-08 1.8388313E-08 midg,1,midg; midg,igrid,midg 1.9231178E-08 2.5884127E-08 1,midg,midg; igrid,midg,midg 4.3877574E-08 9.4812567E-09 gauss-seidel spectral radius is 0.9877369 estimated iterations to convergence 74 setup time was (sec) 0.5000000 now iterating at: 22:15:08 rms-change max change #iterations 0.1426524 25.33600 at 10iterations 1.4613280E-02 2.131302 at 20iterations 1.5324586E-03 0.2255859 at 30iterations 1.8716598E-04 3.1591415E-02 at 40iterations 3.1779098E-05 4.7779083E-03 at 50iterations finished qdiffx linear iterations at : 22:15:10 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.1779098E-05 4.7779083E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 22:15:11 3.348u 0.183s 0:03.81 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 Sat Oct 8 2011 at 22:15:11 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2242 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.951968 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): -14.77600 27.69600 ymin,ymax (A): -11.92900 42.12100 zmin,zma (A): -4.6999931E-02 54.66700 x,y,z range (A): 42.47200 54.05000 54.71400 scale (grids/A): 1.951968 object centre (A): 6.460001 15.09600 27.31000 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 11.51402 assigned positive charge : 328.2416 centred at (gu) : 85.44658 93.62574 87.68971 assigned negative charge : -316.7282 centred at (gu) : 85.67590 93.67786 87.71241 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21416 grid for indexing accessible points = 1.400000 m= 26294 mr = 46444 m= 4795 mr = 18891 m= 348 mr = 2891 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 32879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 16646 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) : 0.6506561 object centre at (A) : 6.460001 15.09600 27.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2861972E-02 5.0404496E-02 midg,1,midg; midg,igrid,midg 4.4538993E-02 2.7825212E-02 1,midg,midg; igrid,midg,midg 3.3741716E-02 -2.2463757E-03 gauss-seidel spectral radius is 0.9986719 estimated iterations to convergence 217 setup time was (sec) 0.8200000 now iterating at: 22:15:12 rms-change max change #iterations 3.978703 180.7790 at 10iterations 1.876848 66.31842 at 20iterations 0.8880063 29.23190 at 30iterations 0.4173688 13.53497 at 40iterations 0.1977527 7.060226 at 50iterations 9.3408488E-02 2.938127 at 60iterations 4.4244442E-02 1.439042 at 70iterations 2.0811211E-02 0.7372780 at 80iterations 9.8824510E-03 0.3248672 at 90iterations 4.6758922E-03 0.1383648 at 100iterations 2.2269723E-03 7.1709633E-02 at 110iterations 1.0683734E-03 3.6656380E-02 at 120iterations finished qdiffx linear iterations at : 22:15:19 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.0683734E-03 3.6656380E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 22:15:19 7.870u 0.243s 0:08.39 96.6% 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 Sat Oct 8 2011 at 22:15:19 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2242 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.927953 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): -14.77600 27.69600 ymin,ymax (A): -11.92900 42.12100 zmin,zma (A): -4.6999931E-02 54.66700 x,y,z range (A): 42.47200 54.05000 54.71400 scale (grids/A): 2.927953 object centre (A): 6.460001 15.09600 27.31000 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 11.51402 assigned positive charge : 328.2416 centred at (gu) : 83.16994 95.43850 86.53432 assigned negative charge : -316.7282 centred at (gu) : 83.51385 95.51690 86.56864 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 160972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21416 grid for indexing accessible points = 1.400000 m= 82311 mr = 112946 m= 32509 mr = 65922 m= 8672 mr = 25631 m= 1504 mr = 6253 m= 133 mr = 1006 m= 0 mr = 55 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 74288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 16864 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) : 1.951968 object centre at (A) : 6.460001 15.09600 27.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6140652 0.5575880 midg,1,midg; midg,igrid,midg 0.5380329 0.3296219 1,midg,midg; igrid,midg,midg 0.3287023 -1.4959251E-02 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 1.620000 now iterating at: 22:15:21 rms-change max change #iterations 9.449224 471.1508 at 10iterations 5.596707 145.8843 at 20iterations 3.301575 83.55463 at 30iterations 1.932502 43.80485 at 40iterations 1.128105 27.03320 at 50iterations 0.6598148 16.44852 at 60iterations 0.3841634 9.133602 at 70iterations 0.2229199 4.707291 at 80iterations 0.1295258 2.728515 at 90iterations 7.5348265E-02 1.958258 at 100iterations 4.3665648E-02 0.8925171 at 110iterations 2.5288941E-02 0.5153542 at 120iterations 1.4669234E-02 0.2858410 at 130iterations 8.5252607E-03 0.1543523 at 140iterations 4.9539101E-03 9.9458456E-02 at 150iterations 2.8943548E-03 5.5736542E-02 at 160iterations 1.7072950E-03 3.2657623E-02 at 170iterations 1.0209582E-03 2.0098686E-02 at 180iterations finished qdiffx linear iterations at : 22:15:33 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 1.0209582E-03 2.0098686E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 22:15:33 13.120u 0.270s 0:13.66 98.0% 0+0k 0+0io 0pf+0w