Sun Oct 9 12:53:01 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 12:53:01 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 = 2405 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6940383 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): -6.325000 41.82400 ymin,ymax (A): -14.13300 37.16100 zmin,zma (A): 2.031000 44.77400 x,y,z range (A): 48.14900 51.29400 42.74300 scale (grids/A): 0.6940383 object centre (A): 17.74950 11.51400 23.40250 number of atom coordinates read : 2405 total number of charged atoms : 2263 net assigned charge : 3.500014 assigned positive charge : 367.9929 centred at (gu) : 90.27703 91.28162 90.75671 assigned negative charge : -364.4934 centred at (gu) : 90.30473 91.44406 90.89315 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7840 nv = 96 ne = 84 npr = 47791 no. pairs analyzed = 47791 no. exposed pairs = 3040 no. arc points = 21042 no. surface atoms = 1019 nbur = 1386 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4355 m= 0 mr = 87 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2900000 number of dielectric boundary points 3911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1999 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8895 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8926902E-08 -4.2004565E-08 midg,1,midg; midg,igrid,midg 7.0423013E-08 -6.1788178E-08 1,midg,midg; igrid,midg,midg 3.2870165E-08 1.1746518E-08 gauss-seidel spectral radius is 0.9892153 estimated iterations to convergence 78 setup time was (sec) 0.5000000 now iterating at: 12:53:02 rms-change max change #iterations 0.1948460 27.49686 at 10iterations 2.3879454E-02 3.369892 at 20iterations 3.4310126E-03 0.4661310 at 30iterations 8.1386091E-04 0.1199837 at 40iterations 2.7675126E-04 4.1734695E-02 at 50iterations finished qdiffx linear iterations at : 12:53:04 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.7675126E-04 4.1734695E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 12:53:05 3.089u 0.138s 0:03.54 90.6% 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 Sun Oct 9 2011 at 12:53:05 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 = 2405 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.082115 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): -6.325000 41.82400 ymin,ymax (A): -14.13300 37.16100 zmin,zma (A): 2.031000 44.77400 x,y,z range (A): 48.14900 51.29400 42.74300 scale (grids/A): 2.082115 object centre (A): 17.74950 11.51400 23.40250 number of atom coordinates read : 2405 total number of charged atoms : 2263 net assigned charge : 3.500014 assigned positive charge : 367.9929 centred at (gu) : 90.83052 93.84433 92.26974 assigned negative charge : -364.4934 centred at (gu) : 90.91399 94.33196 92.67911 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21042 grid for indexing accessible points = 1.400000 m= 32616 mr = 58026 m= 6222 mr = 24398 m= 552 mr = 4030 m= 14 mr = 293 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 330 time to turn everything in is 0.5900000 number of dielectric boundary points 35799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17978 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) : 0.6940383 object centre at (A) : 17.74950 11.51400 23.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0524037E-02 2.3471862E-03 midg,1,midg; midg,igrid,midg 2.0253077E-02 -5.1373817E-02 1,midg,midg; igrid,midg,midg 5.2457988E-02 -5.0897822E-03 gauss-seidel spectral radius is 0.9988291 estimated iterations to convergence 231 setup time was (sec) 0.8600000 now iterating at: 12:53:06 rms-change max change #iterations 4.860371 200.2206 at 10iterations 2.401731 77.16180 at 20iterations 1.187884 42.92215 at 30iterations 0.5881656 17.54252 at 40iterations 0.2920043 10.10336 at 50iterations 0.1450347 4.097581 at 60iterations 7.1925484E-02 2.091969 at 70iterations 3.5953104E-02 1.062389 at 80iterations 1.7999392E-02 0.5192585 at 90iterations 9.1011496E-03 0.2744789 at 100iterations 4.6992293E-03 0.1282964 at 110iterations 2.5236260E-03 8.5861206E-02 at 120iterations finished qdiffx linear iterations at : 12:53:12 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 2.5236260E-03 8.5861206E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 12:53:13 7.109u 0.158s 0:07.58 95.6% 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 Sun Oct 9 2011 at 12:53:13 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 = 2405 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: 3.123172 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): -6.325000 41.82400 ymin,ymax (A): -14.13300 37.16100 zmin,zma (A): 2.031000 44.77400 x,y,z range (A): 48.14900 51.29400 42.74300 scale (grids/A): 3.123172 object centre (A): 17.74950 11.51400 23.40250 number of atom coordinates read : 2405 total number of charged atoms : 2263 net assigned charge : 3.500014 assigned positive charge : 367.9929 centred at (gu) : 91.24565 95.76627 93.40452 assigned negative charge : -364.4934 centred at (gu) : 91.37096 96.49783 94.01859 start vw surface at 0.1500000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 191768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21042 grid for indexing accessible points = 1.400000 m= 101966 mr = 140325 m= 40744 mr = 83782 m= 11453 mr = 33173 m= 2396 mr = 8742 m= 275 mr = 1799 m= 7 mr = 173 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1130 time to turn everything in is 1.820000 number of dielectric boundary points 80615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 18104 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) : 2.082115 object centre at (A) : 17.74950 11.51400 23.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4645266 -2.6648315E-02 midg,1,midg; midg,igrid,midg 0.4042827 -0.4992174 1,midg,midg; igrid,midg,midg 0.7671286 -0.3177571 gauss-seidel spectral radius is 0.9993013 estimated iterations to convergence 298 setup time was (sec) 2.120000 now iterating at: 12:53:15 rms-change max change #iterations 11.01146 466.2848 at 10iterations 6.557985 152.1260 at 20iterations 3.885620 79.92722 at 30iterations 2.303339 40.69822 at 40iterations 1.363958 24.63877 at 50iterations 0.8043667 14.89212 at 60iterations 0.4749696 8.415749 at 70iterations 0.2784981 5.114887 at 80iterations 0.1643166 3.175673 at 90iterations 9.6422270E-02 1.593358 at 100iterations 5.6698244E-02 1.038871 at 110iterations 3.3555169E-02 0.5626011 at 120iterations 1.9997405E-02 0.3885002 at 130iterations 1.2091061E-02 0.2166100 at 140iterations 7.5240964E-03 0.1347294 at 150iterations 4.9116085E-03 0.1046486 at 160iterations 3.3924603E-03 7.0205688E-02 at 170iterations 2.5068880E-03 5.0338745E-02 at 180iterations finished qdiffx linear iterations at : 12:53:24 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 2.5068880E-03 5.0338745E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 12:53:25 11.861u 0.163s 0:12.28 97.8% 0+0k 0+0io 0pf+0w