Sat Oct 8 12:24:24 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 12:24:24 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3021 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: 0.5090004 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): -60.11600 9.825000 ymin,ymax (A): -37.87400 17.89900 zmin,zma (A): -4.446000 56.94200 x,y,z range (A): 69.94100 55.77300 61.38800 scale (grids/A): 0.5090004 object centre (A): -25.14550 -9.987500 26.24800 number of atom coordinates read : 3021 total number of charged atoms : 2882 net assigned charge : -0.9999670 assigned positive charge : 418.7923 centred at (gu) : 93.42170 89.47851 89.18267 assigned negative charge : -419.7933 centred at (gu) : 93.27177 89.41896 89.16224 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5212 nv = 96 ne = 84 npr = 60789 no. pairs analyzed = 60789 no. exposed pairs = 4458 no. arc points = 31780 no. surface atoms = 1489 nbur = 1532 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 220 mr = 2181 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3042 ## 395 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0674403E-11 6.6750329E-12 midg,1,midg; midg,igrid,midg -1.1977672E-10 5.4404963E-11 1,midg,midg; igrid,midg,midg -9.5466822E-11 4.7528914E-10 gauss-seidel spectral radius is 0.9801580 estimated iterations to convergence 59 setup time was (sec) 0.6800000 now iterating at: 12:24:25 rms-change max change #iterations 4.9029317E-02 9.449390 at 10iterations 4.9256035E-03 1.132595 at 20iterations 1.5677199E-03 0.3813629 at 30iterations 5.8571633E-04 0.1416092 at 40iterations 2.1888324E-04 5.2974701E-02 at 50iterations finished qdiffx linear iterations at : 12:24:30 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 2.1888324E-04 5.2974701E-02 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.350000 DelPhi exited at 12:24:30 5.354u 0.449s 0:06.05 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 Sat Oct 8 2011 at 12:24:30 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3021 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: 1.527001 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): -60.11600 9.825000 ymin,ymax (A): -37.87400 17.89900 zmin,zma (A): -4.446000 56.94200 x,y,z range (A): 69.94100 55.77300 61.38800 scale (grids/A): 1.527001 object centre (A): -25.14550 -9.987500 26.24800 number of atom coordinates read : 3021 total number of charged atoms : 2882 net assigned charge : -0.9999670 assigned positive charge : 418.7923 centred at (gu) : 100.2642 88.43460 87.54745 assigned negative charge : -419.7933 centred at (gu) : 99.81506 88.25665 87.48654 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31780 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15367 mr = 35367 m= 1418 mr = 8783 m= 29 mr = 451 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 30455 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21777 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) : 0.5090004 object centre at (A) : -25.14550 -9.987500 26.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8490520E-03 5.3098071E-03 midg,1,midg; midg,igrid,midg -3.0579029E-03 2.4580648E-03 1,midg,midg; igrid,midg,midg -3.4787562E-03 3.4404041E-03 gauss-seidel spectral radius is 0.9979365 estimated iterations to convergence 175 setup time was (sec) 0.8900000 now iterating at: 12:24:32 rms-change max change #iterations 2.756250 175.4390 at 10iterations 1.071267 47.19360 at 20iterations 0.4190089 16.74661 at 30iterations 0.1646095 6.918585 at 40iterations 6.4911768E-02 2.648363 at 50iterations 2.6149310E-02 1.003647 at 60iterations 1.1133340E-02 0.5456238 at 70iterations 5.3349915E-03 0.2593861 at 80iterations 3.0103999E-03 0.1563606 at 90iterations 1.9706090E-03 9.4841003E-02 at 100iterations 1.3723831E-03 6.6623688E-02 at 110iterations 9.7642676E-04 4.7691345E-02 at 120iterations finished qdiffx linear iterations at : 12:24:43 total time elapsed so far: 12.01000 # loops : 120 mean,max change (kT/e) : 9.7642676E-04 4.7691345E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 12:24:44 12.237u 0.508s 0:13.06 97.4% 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 12:24:44 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3021 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: 2.290502 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): -60.11600 9.825000 ymin,ymax (A): -37.87400 17.89900 zmin,zma (A): -4.446000 56.94200 x,y,z range (A): 69.94100 55.77300 61.38800 scale (grids/A): 2.290502 object centre (A): -25.14550 -9.987500 26.24800 number of atom coordinates read : 3021 total number of charged atoms : 2882 net assigned charge : -0.9999670 assigned positive charge : 418.7923 centred at (gu) : 105.3962 87.65166 86.32096 assigned negative charge : -419.7933 centred at (gu) : 104.7225 87.38480 86.22973 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 135707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31780 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 54149 mr = 88944 m= 13623 mr = 38042 m= 1834 mr = 8760 m= 73 mr = 956 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 68682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 22993 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) : 1.527001 object centre at (A) : -25.14550 -9.987500 26.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6119708E-04 8.9206770E-02 midg,1,midg; midg,igrid,midg -5.1515855E-02 4.7142588E-02 1,midg,midg; igrid,midg,midg -3.7526499E-02 8.0122232E-02 gauss-seidel spectral radius is 0.9990626 estimated iterations to convergence 258 setup time was (sec) 1.670000 now iterating at: 12:24:46 rms-change max change #iterations 7.656676 257.6447 at 10iterations 4.293778 129.3327 at 20iterations 2.384859 74.71028 at 30iterations 1.311907 35.37030 at 40iterations 0.7173973 17.16947 at 50iterations 0.3905172 10.17183 at 60iterations 0.2124155 4.799800 at 70iterations 0.1151997 2.700842 at 80iterations 6.2406279E-02 1.758528 at 90iterations 3.3705045E-02 0.8435541 at 100iterations 1.8229103E-02 0.4272928 at 110iterations 9.9164834E-03 0.2220917 at 120iterations 5.4064379E-03 0.1237221 at 130iterations 3.0176684E-03 8.7112427E-02 at 140iterations 1.7524157E-03 4.3876648E-02 at 150iterations 1.0815139E-03 3.1366348E-02 at 160iterations 7.2351791E-04 1.9359589E-02 at 170iterations 5.2034424E-04 1.5144348E-02 at 180iterations finished qdiffx linear iterations at : 12:25:04 total time elapsed so far: 20.21000 # loops : 180 mean,max change (kT/e) : 5.2034424E-04 1.5144348E-02 energy calculations done at 20.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.39000 DelPhi exited at 12:25:05 20.392u 0.527s 0:21.18 98.7% 0+0k 0+0io 0pf+0w