Sat Oct 15 12:24:20 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 Sat Oct 15 2011 at 12:24:20 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5353 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5033225 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): 2.675000 73.40500 ymin,ymax (A): -10.32900 48.50900 zmin,zma (A): -7.890000 60.45700 x,y,z range (A): 70.73000 58.83800 68.34700 scale (grids/A): 0.5033225 object centre (A): 38.04000 19.09000 26.28350 number of atom coordinates read : 5353 total number of charged atoms : 5152 net assigned charge : 14.49998 assigned positive charge : 801.4751 centred at (gu) : 88.57162 90.86529 90.45837 assigned negative charge : -786.9821 centred at (gu) : 88.52674 90.91307 90.42406 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8537 nv = 96 ne = 84 npr = 107569 no. pairs analyzed = 107569 no. exposed pairs = 6759 no. arc points = 46480 no. surface atoms = 2260 nbur = 3093 mkacc time = 0.2800000 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 = 1.708000 m= 314 mr = 4440 m= 0 mr = 11 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4437 ## 635 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 11474 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9633369E-11 2.4895544E-10 midg,1,midg; midg,igrid,midg 1.9775392E-10 6.1046668E-11 1,midg,midg; igrid,midg,midg 7.8822004E-11 1.6670977E-10 gauss-seidel spectral radius is 0.9798566 estimated iterations to convergence 58 setup time was (sec) 0.8800000 now iterating at: 12:24:21 rms-change max change #iterations 6.4696856E-02 11.02047 at 10iterations 5.9799552E-03 0.8229218 at 20iterations 1.8194900E-03 0.2466621 at 30iterations 6.8416103E-04 8.5834503E-02 at 40iterations 2.6174428E-04 3.1105042E-02 at 50iterations finished qdiffx linear iterations at : 12:24:26 total time elapsed so far: 5.380000 # loops : 50 mean,max change (kT/e) : 2.6174428E-04 3.1105042E-02 energy calculations done at 5.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.550000 DelPhi exited at 12:24:27 5.550u 0.489s 0:06.48 93.0% 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 15 2011 at 12:24:27 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5353 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.509968 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): 2.675000 73.40500 ymin,ymax (A): -10.32900 48.50900 zmin,zma (A): -7.890000 60.45700 x,y,z range (A): 70.73000 58.83800 68.34700 scale (grids/A): 1.509968 object centre (A): 38.04000 19.09000 26.28350 number of atom coordinates read : 5353 total number of charged atoms : 5152 net assigned charge : 14.49998 assigned positive charge : 801.4751 centred at (gu) : 85.71281 92.59370 91.37335 assigned negative charge : -786.9821 centred at (gu) : 85.57967 92.73849 91.27166 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 97743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27560 mr = 67463 m= 2218 mr = 17982 m= 44 mr = 899 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 41221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 566 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 38485 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) : 0.5033225 object centre at (A) : 38.04000 19.09000 26.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2360197E-02 5.2743964E-03 midg,1,midg; midg,igrid,midg 9.1837291E-03 7.2829514E-03 1,midg,midg; igrid,midg,midg 3.8432363E-02 2.9601453E-02 gauss-seidel spectral radius is 0.9981099 estimated iterations to convergence 183 setup time was (sec) 1.200000 now iterating at: 12:24:28 rms-change max change #iterations 3.890995 183.9272 at 10iterations 1.586997 54.57373 at 20iterations 0.6501271 20.00341 at 30iterations 0.2654243 8.291351 at 40iterations 0.1096423 3.303174 at 50iterations 4.5251764E-02 1.386257 at 60iterations 1.9043427E-02 0.5638599 at 70iterations 8.3623054E-03 0.2840786 at 80iterations 3.9387750E-03 0.1153488 at 90iterations 2.1160529E-03 6.5147400E-02 at 100iterations 1.2837392E-03 3.3424377E-02 at 110iterations 8.4519613E-04 2.0877838E-02 at 120iterations finished qdiffx linear iterations at : 12:24:40 total time elapsed so far: 12.84000 # loops : 120 mean,max change (kT/e) : 8.4519613E-04 2.0877838E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 12:24:40 13.019u 0.530s 0:13.83 97.9% 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 15 2011 at 12:24:40 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5353 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.264951 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): 2.675000 73.40500 ymin,ymax (A): -10.32900 48.50900 zmin,zma (A): -7.890000 60.45700 x,y,z range (A): 70.73000 58.83800 68.34700 scale (grids/A): 2.264951 object centre (A): 38.04000 19.09000 26.28350 number of atom coordinates read : 5353 total number of charged atoms : 5152 net assigned charge : 14.49998 assigned positive charge : 801.4751 centred at (gu) : 83.56860 93.89016 92.05963 assigned negative charge : -786.9821 centred at (gu) : 83.36932 94.10775 91.90755 start vw surface at 0.2100000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 228111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 99897 mr = 166125 m= 24168 mr = 77287 m= 3087 mr = 17159 m= 131 mr = 1794 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 93004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 41060 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) : 1.509968 object centre at (A) : 38.04000 19.09000 26.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2622652 0.1483645 midg,1,midg; midg,igrid,midg 0.1668452 0.1439845 1,midg,midg; igrid,midg,midg 0.6663938 0.7405514 gauss-seidel spectral radius is 0.9991750 estimated iterations to convergence 275 setup time was (sec) 2.500000 now iterating at: 12:24:43 rms-change max change #iterations 10.67990 255.7112 at 10iterations 6.162194 171.5973 at 20iterations 3.545717 78.75363 at 30iterations 2.015794 52.40245 at 40iterations 1.144722 24.38537 at 50iterations 0.6454867 14.54450 at 60iterations 0.3637641 6.917696 at 70iterations 0.2048821 3.629051 at 80iterations 0.1151796 2.361853 at 90iterations 6.4495191E-02 1.272917 at 100iterations 3.6308687E-02 0.6864796 at 110iterations 2.0374179E-02 0.3872147 at 120iterations 1.1472643E-02 0.2005386 at 130iterations 6.4985533E-03 0.1189423 at 140iterations 3.7268566E-03 6.9067955E-02 at 150iterations 2.1843868E-03 4.1016579E-02 at 160iterations 1.3250124E-03 2.3269653E-02 at 170iterations 8.4311829E-04 1.5322685E-02 at 180iterations finished qdiffx linear iterations at : 12:25:04 total time elapsed so far: 22.79000 # loops : 180 mean,max change (kT/e) : 8.4311829E-04 1.5322685E-02 energy calculations done at 22.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.96000 DelPhi exited at 12:25:04 22.968u 0.533s 0:23.89 98.3% 0+0k 0+0io 0pf+0w