Tue Oct 11 05:17:28 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 05:17:28 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG5 580 has a net charge of 1.4000 !!! WARNING: ZN5 581 has a net charge of 1.4000 !!! WARNING: ZN5 582 has a net charge of 1.4000 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 0.6892279 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): 15.66400 62.96400 ymin,ymax (A): -3.632000 34.14100 zmin,zma (A): 20.07800 71.73000 x,y,z range (A): 47.30000 37.77300 51.65200 scale (grids/A): 0.6892279 object centre (A): 39.31400 15.25450 45.90400 number of atom coordinates read : 2327 total number of charged atoms : 2003 net assigned charge : 11.80001 assigned positive charge : 330.7108 centred at (gu) : 91.50431 89.53186 89.11517 assigned negative charge : -318.9111 centred at (gu) : 91.58011 89.47222 88.99760 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6812 nv = 96 ne = 84 npr = 42669 no. pairs analyzed = 42669 no. exposed pairs = 2604 no. arc points = 17656 no. surface atoms = 889 nbur = 1438 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 3938 m= 4 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1693 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9519462E-08 8.6881137E-08 midg,1,midg; midg,igrid,midg 4.8992277E-08 7.7087037E-08 1,midg,midg; igrid,midg,midg 6.7008742E-08 5.2206218E-08 gauss-seidel spectral radius is 0.9890357 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 05:17:29 rms-change max change #iterations 0.1895566 26.85890 at 10iterations 2.1846913E-02 2.897512 at 20iterations 2.5976116E-03 0.3799009 at 30iterations 3.1054212E-04 4.1246414E-02 at 40iterations 3.9467068E-05 6.0234070E-03 at 50iterations finished qdiffx linear iterations at : 05:17:31 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 3.9467068E-05 6.0234070E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 05:17:32 3.313u 0.174s 0:04.06 85.7% 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 05:17:32 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG5 580 has a net charge of 1.4000 !!! WARNING: ZN5 581 has a net charge of 1.4000 !!! WARNING: ZN5 582 has a net charge of 1.4000 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 2.067683 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): 15.66400 62.96400 ymin,ymax (A): -3.632000 34.14100 zmin,zma (A): 20.07800 71.73000 x,y,z range (A): 47.30000 37.77300 51.65200 scale (grids/A): 2.067683 object centre (A): 39.31400 15.25450 45.90400 number of atom coordinates read : 2327 total number of charged atoms : 2003 net assigned charge : 11.80001 assigned positive charge : 330.7108 centred at (gu) : 94.51299 88.59545 87.34532 assigned negative charge : -318.9111 centred at (gu) : 94.74040 88.41675 86.99277 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17656 grid for indexing accessible points = 1.400000 m= 29124 mr = 51662 m= 5476 mr = 22147 m= 453 mr = 3699 m= 12 mr = 222 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.3700000 number of dielectric boundary points 29899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 15859 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) : 0.6892279 object centre at (A) : 39.31400 15.25450 45.90400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7213458E-02 5.7227224E-02 midg,1,midg; midg,igrid,midg 3.0535946E-02 4.4473950E-02 1,midg,midg; igrid,midg,midg 2.7436618E-02 4.0678181E-02 gauss-seidel spectral radius is 0.9987799 estimated iterations to convergence 227 setup time was (sec) 0.5800000 now iterating at: 05:17:33 rms-change max change #iterations 4.488274 196.1092 at 10iterations 2.200158 79.85557 at 20iterations 1.067147 31.99299 at 30iterations 0.5225670 15.98600 at 40iterations 0.2550445 8.166700 at 50iterations 0.1250426 3.678551 at 60iterations 6.1341915E-02 1.878204 at 70iterations 2.9866233E-02 0.9390182 at 80iterations 1.4582985E-02 0.4731598 at 90iterations 7.1398942E-03 0.2217197 at 100iterations 3.4941263E-03 0.1084778 at 110iterations 1.7073703E-03 5.6913376E-02 at 120iterations finished qdiffx linear iterations at : 05:17:40 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.7073703E-03 5.6913376E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 05:17:40 7.779u 0.209s 0:08.32 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 05:17:40 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG5 580 has a net charge of 1.4000 !!! WARNING: ZN5 581 has a net charge of 1.4000 !!! WARNING: ZN5 582 has a net charge of 1.4000 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 3.101525 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): 15.66400 62.96400 ymin,ymax (A): -3.632000 34.14100 zmin,zma (A): 20.07800 71.73000 x,y,z range (A): 47.30000 37.77300 51.65200 scale (grids/A): 3.101525 object centre (A): 39.31400 15.25450 45.90400 number of atom coordinates read : 2327 total number of charged atoms : 2003 net assigned charge : 11.80001 assigned positive charge : 330.7108 centred at (gu) : 96.76928 87.89319 86.01796 assigned negative charge : -318.9111 centred at (gu) : 97.11052 87.62513 85.48923 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17656 grid for indexing accessible points = 1.400000 m= 90758 mr = 124163 m= 36596 mr = 75706 m= 10352 mr = 30178 m= 1911 mr = 8085 m= 184 mr = 1414 m= 3 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 570 time to turn everything in is 1.120000 number of dielectric boundary points 67465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 16023 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) : 2.067683 object centre at (A) : 39.31400 15.25450 45.90400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4351732 0.4436055 midg,1,midg; midg,igrid,midg 0.2621072 0.3968988 1,midg,midg; igrid,midg,midg 0.2275180 0.5935910 gauss-seidel spectral radius is 0.9992835 estimated iterations to convergence 295 setup time was (sec) 1.350000 now iterating at: 05:17:42 rms-change max change #iterations 10.16759 380.0702 at 10iterations 5.993102 132.6999 at 20iterations 3.518042 87.93566 at 30iterations 2.066123 39.87012 at 40iterations 1.209694 25.62407 at 50iterations 0.7091229 17.46096 at 60iterations 0.4142645 7.707907 at 70iterations 0.2419224 5.633335 at 80iterations 0.1410015 2.707922 at 90iterations 8.2122006E-02 1.745823 at 100iterations 4.7879249E-02 0.9707375 at 110iterations 2.7902605E-02 0.5448933 at 120iterations 1.6230300E-02 0.2987287 at 130iterations 9.4742384E-03 0.1614914 at 140iterations 5.5254325E-03 9.8284721E-02 at 150iterations 3.2278595E-03 6.1636925E-02 at 160iterations 1.8952979E-03 3.4959793E-02 at 170iterations 1.1227655E-03 1.9806147E-02 at 180iterations finished qdiffx linear iterations at : 05:17:53 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 1.1227655E-03 1.9806147E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 05:17:54 12.717u 0.205s 0:13.20 97.8% 0+0k 0+0io 0pf+0w