Mon Oct 10 12:13:15 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 Mon Oct 10 2011 at 12:13:15 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7416975 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): 8.332001 56.33000 ymin,ymax (A): -9.149000 36.52500 zmin,zma (A): -2.976000 44.17600 x,y,z range (A): 47.99800 45.67400 47.15200 scale (grids/A): 0.7416975 object centre (A): 32.33100 13.68800 20.60000 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 320.1998 centred at (gu) : 89.51303 90.47910 89.88383 assigned negative charge : -326.5720 centred at (gu) : 89.51892 90.56097 90.06375 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8038 nv = 96 ne = 84 npr = 43059 no. pairs analyzed = 43059 no. exposed pairs = 2738 no. arc points = 19223 no. surface atoms = 932 nbur = 1185 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 578 mr = 4461 m= 3 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1611 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5509455E-08 -3.0578815E-07 midg,1,midg; midg,igrid,midg -2.6990223E-08 -2.2363503E-07 1,midg,midg; igrid,midg,midg -1.1979245E-07 -1.1214357E-07 gauss-seidel spectral radius is 0.9905291 estimated iterations to convergence 83 setup time was (sec) 0.5800000 now iterating at: 12:13:16 rms-change max change #iterations 0.2512745 34.52718 at 10iterations 3.4764890E-02 4.209808 at 20iterations 4.6517933E-03 0.5711861 at 30iterations 6.3268095E-04 8.4663391E-02 at 40iterations 8.4460560E-05 1.1006355E-02 at 50iterations finished qdiffx linear iterations at : 12:13:19 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 8.4460560E-05 1.1006355E-02 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 12:13:20 4.452u 0.392s 0:05.26 92.0% 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 Mon Oct 10 2011 at 12:13:20 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.225093 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): 8.332001 56.33000 ymin,ymax (A): -9.149000 36.52500 zmin,zma (A): -2.976000 44.17600 x,y,z range (A): 47.99800 45.67400 47.15200 scale (grids/A): 2.225093 object centre (A): 32.33100 13.68800 20.60000 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 320.1998 centred at (gu) : 88.53908 91.43710 89.65154 assigned negative charge : -326.5720 centred at (gu) : 88.55701 91.68291 90.19103 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19223 grid for indexing accessible points = 1.400000 m= 34017 mr = 58110 m= 7202 mr = 25962 m= 753 mr = 4955 m= 19 mr = 393 m= 0 mr = 3 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 37141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15769 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) : 0.7416975 object centre at (A) : 32.33100 13.68800 20.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4515897E-03 -0.1191468 midg,1,midg; midg,igrid,midg -3.3471733E-02 -5.3401183E-02 1,midg,midg; igrid,midg,midg -6.2378580E-03 6.7104339E-03 gauss-seidel spectral radius is 0.9989323 estimated iterations to convergence 242 setup time was (sec) 1.010000 now iterating at: 12:13:22 rms-change max change #iterations 5.187891 206.8746 at 10iterations 2.635898 79.58600 at 20iterations 1.343942 38.12943 at 30iterations 0.6870356 19.15131 at 40iterations 0.3514010 10.49394 at 50iterations 0.1795481 5.972816 at 60iterations 9.1700286E-02 2.823608 at 70iterations 4.6885941E-02 1.389208 at 80iterations 2.3922758E-02 0.6757784 at 90iterations 1.2257261E-02 0.3368359 at 100iterations 6.2602856E-03 0.1874390 at 110iterations 3.2006924E-03 8.8298798E-02 at 120iterations finished qdiffx linear iterations at : 12:13:32 total time elapsed so far: 11.27000 # loops : 120 mean,max change (kT/e) : 3.2006924E-03 8.8298798E-02 energy calculations done at 11.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 12:13:33 11.452u 0.442s 0:12.89 92.2% 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 Mon Oct 10 2011 at 12:13:33 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.337639 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): 8.332001 56.33000 ymin,ymax (A): -9.149000 36.52500 zmin,zma (A): -2.976000 44.17600 x,y,z range (A): 47.99800 45.67400 47.15200 scale (grids/A): 3.337639 object centre (A): 32.33100 13.68800 20.60000 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 320.1998 centred at (gu) : 87.80862 92.15549 89.47737 assigned negative charge : -326.5720 centred at (gu) : 87.83556 92.52449 90.28664 start vw surface at 0.1000000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 194403 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19223 grid for indexing accessible points = 1.400000 m= 104191 mr = 140043 m= 44823 mr = 86235 m= 13878 mr = 37196 m= 3017 mr = 10980 m= 436 mr = 2267 m= 16 mr = 285 m= 0 mr = 8 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.250000 number of dielectric boundary points 83750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 15824 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) : 2.225093 object centre at (A) : 32.33100 13.68800 20.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1123849 -1.155258 midg,1,midg; midg,igrid,midg -0.2894942 -0.2832734 1,midg,midg; igrid,midg,midg -0.1127381 -2.6264593E-02 gauss-seidel spectral radius is 0.9993221 estimated iterations to convergence 303 setup time was (sec) 2.600000 now iterating at: 12:13:36 rms-change max change #iterations 11.29080 362.3301 at 10iterations 6.673193 129.1743 at 20iterations 3.957464 68.77605 at 30iterations 2.333953 44.04991 at 40iterations 1.376131 23.20329 at 50iterations 0.8134297 13.74870 at 60iterations 0.4786487 7.707941 at 70iterations 0.2820785 4.913147 at 80iterations 0.1659783 2.697077 at 90iterations 9.7635582E-02 1.801918 at 100iterations 5.7462752E-02 1.027600 at 110iterations 3.3835862E-02 0.5214767 at 120iterations 1.9930722E-02 0.3149414 at 130iterations 1.1681421E-02 0.2031741 at 140iterations 6.8973633E-03 0.1143055 at 150iterations 4.0514995E-03 6.3699722E-02 at 160iterations 2.3843567E-03 3.7981033E-02 at 170iterations 1.4016381E-03 2.3566961E-02 at 180iterations finished qdiffx linear iterations at : 12:13:54 total time elapsed so far: 20.06000 # loops : 180 mean,max change (kT/e) : 1.4016381E-03 2.3566961E-02 energy calculations done at 20.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.22000 DelPhi exited at 12:13:54 20.229u 0.494s 0:21.08 98.2% 0+0k 0+0io 0pf+0w