Tue Oct 11 06:38:10 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 06:38:10 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 = 2046 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: 0.7007874 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): -20.23600 24.50400 ymin,ymax (A): -26.67100 10.64800 zmin,zma (A): -14.12400 36.67600 x,y,z range (A): 44.74000 37.31900 50.80000 scale (grids/A): 0.7007874 object centre (A): 2.134000 -8.011499 11.27600 number of atom coordinates read : 2046 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 89.74651 90.93553 89.29081 assigned negative charge : -305.3172 centred at (gu) : 89.57356 90.92331 89.26609 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6820 nv = 96 ne = 84 npr = 40916 no. pairs analyzed = 40916 no. exposed pairs = 2474 no. arc points = 17177 no. surface atoms = 844 nbur = 1202 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 3909 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1580 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7662 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0172769E-08 5.6334926E-08 midg,1,midg; midg,igrid,midg 4.1240408E-08 7.0963289E-08 1,midg,midg; igrid,midg,midg -2.0169237E-08 1.1890148E-07 gauss-seidel spectral radius is 0.9893840 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 06:38:11 rms-change max change #iterations 0.1882840 25.66017 at 10iterations 2.3102347E-02 3.120766 at 20iterations 2.8693131E-03 0.3797684 at 30iterations 3.8951656E-04 5.7430267E-02 at 40iterations 7.0949434E-05 1.0760784E-02 at 50iterations finished qdiffx linear iterations at : 06:38:14 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 7.0949434E-05 1.0760784E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 06:38:15 3.406u 0.166s 0:04.24 83.9% 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 Tue Oct 11 2011 at 06:38:15 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 = 2046 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: 2.102362 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): -20.23600 24.50400 ymin,ymax (A): -26.67100 10.64800 zmin,zma (A): -14.12400 36.67600 x,y,z range (A): 44.74000 37.31900 50.80000 scale (grids/A): 2.102362 object centre (A): 2.134000 -8.011499 11.27600 number of atom coordinates read : 2046 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 89.23944 92.80648 87.87222 assigned negative charge : -305.3172 centred at (gu) : 88.72091 92.77012 87.79846 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17177 grid for indexing accessible points = 1.400000 m= 28549 mr = 51364 m= 5360 mr = 21468 m= 480 mr = 3584 m= 6 mr = 246 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 30059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15370 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) : 0.7007874 object centre at (A) : 2.134000 -8.011499 11.27600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7484409E-02 4.6489086E-02 midg,1,midg; midg,igrid,midg 4.9204752E-03 3.4217488E-02 1,midg,midg; igrid,midg,midg 9.5343804E-03 3.5464142E-02 gauss-seidel spectral radius is 0.9988078 estimated iterations to convergence 229 setup time was (sec) 0.8400000 now iterating at: 06:38:16 rms-change max change #iterations 4.407699 179.2078 at 10iterations 2.173001 71.29735 at 20iterations 1.067121 33.74266 at 30iterations 0.5277066 17.19555 at 40iterations 0.2600244 8.021240 at 50iterations 0.1290514 4.099138 at 60iterations 6.3319877E-02 1.987748 at 70iterations 3.1376589E-02 1.024616 at 80iterations 1.5521313E-02 0.5946712 at 90iterations 7.6798857E-03 0.2278671 at 100iterations 3.8223637E-03 0.1305256 at 110iterations 1.9217688E-03 5.9476852E-02 at 120iterations finished qdiffx linear iterations at : 06:38:22 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 1.9217688E-03 5.9476852E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 06:38:23 7.608u 0.186s 0:08.14 95.5% 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 06:38:23 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 = 2046 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: 3.153543 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): -20.23600 24.50400 ymin,ymax (A): -26.67100 10.64800 zmin,zma (A): -14.12400 36.67600 x,y,z range (A): 44.74000 37.31900 50.80000 scale (grids/A): 3.153543 object centre (A): 2.134000 -8.011499 11.27600 number of atom coordinates read : 2046 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 88.85918 94.20978 86.80824 assigned negative charge : -305.3172 centred at (gu) : 88.08133 94.15512 86.69775 start vw surface at 0.1300000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 166834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17177 grid for indexing accessible points = 1.400000 m= 89668 mr = 123536 m= 35717 mr = 74549 m= 10318 mr = 29270 m= 1967 mr = 7991 m= 178 mr = 1442 m= 5 mr = 97 m= 0 mr = 2 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 67800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 15496 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) : 2.102362 object centre at (A) : 2.134000 -8.011499 11.27600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6398401 0.3882330 midg,1,midg; midg,igrid,midg 2.5066035E-02 0.2824191 1,midg,midg; igrid,midg,midg 0.1947988 0.2763980 gauss-seidel spectral radius is 0.9992892 estimated iterations to convergence 296 setup time was (sec) 2.070000 now iterating at: 06:38:25 rms-change max change #iterations 10.00396 342.6774 at 10iterations 5.891862 130.4296 at 20iterations 3.469221 79.49380 at 30iterations 2.039011 40.51789 at 40iterations 1.197688 25.17861 at 50iterations 0.7028093 12.41022 at 60iterations 0.4101213 7.937441 at 70iterations 0.2397809 4.580976 at 80iterations 0.1398946 2.912977 at 90iterations 8.1977837E-02 1.665545 at 100iterations 4.7921419E-02 1.108073 at 110iterations 2.8096877E-02 0.5182343 at 120iterations 1.6508996E-02 0.3168221 at 130iterations 9.7467098E-03 0.1809235 at 140iterations 5.8512297E-03 0.1069231 at 150iterations 3.5652791E-03 6.7768097E-02 at 160iterations 2.2610789E-03 4.6497345E-02 at 170iterations 1.4942647E-03 2.9804230E-02 at 180iterations finished qdiffx linear iterations at : 06:38:36 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 1.4942647E-03 2.9804230E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 06:38:36 13.114u 0.209s 0:13.66 97.4% 0+0k 0+0io 0pf+0w