Mon Oct 10 17:02:26 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 Mon Oct 10 2011 at 17:02:26 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 !!! WARNING: GLU 168 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5870616 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): 17.51500 75.66800 ymin,ymax (A): 5.320000 65.96100 zmin,zma (A): -14.99500 25.17400 x,y,z range (A): 58.15300 60.64100 40.16900 scale (grids/A): 0.5870616 object centre (A): 46.59150 35.64050 5.089500 number of atom coordinates read : 2379 total number of charged atoms : 2247 net assigned charge : -4.999986 assigned positive charge : 341.1185 centred at (gu) : 89.19702 90.51254 90.43560 assigned negative charge : -346.1187 centred at (gu) : 89.14867 90.50675 90.41849 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5533 nv = 96 ne = 84 npr = 48114 no. pairs analyzed = 48114 no. exposed pairs = 3194 no. arc points = 23245 no. surface atoms = 1067 nbur = 1312 mkacc time = 0.1400000 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 = 1.484000 m= 248 mr = 2726 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3600000 number of dielectric boundary points 3042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2367 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 6951 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5904412E-09 -1.1182960E-09 midg,1,midg; midg,igrid,midg -1.3457475E-09 -1.4128523E-09 1,midg,midg; igrid,midg,midg -2.9292690E-09 -2.9793243E-10 gauss-seidel spectral radius is 0.9849805 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 17:02:27 rms-change max change #iterations 9.6226990E-02 18.70245 at 10iterations 7.5736986E-03 1.246887 at 20iterations 6.1193306E-04 9.8714828E-02 at 30iterations 4.9766386E-05 8.2435608E-03 at 40iterations 4.2093548E-06 7.5340271E-04 at 50iterations finished qdiffx linear iterations at : 17:02:30 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 4.2093548E-06 7.5340271E-04 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 17:02:32 4.299u 0.244s 0:05.47 82.8% 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 17:02:32 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 !!! WARNING: GLU 168 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.761185 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): 17.51500 75.66800 ymin,ymax (A): 5.320000 65.96100 zmin,zma (A): -14.99500 25.17400 x,y,z range (A): 58.15300 60.64100 40.16900 scale (grids/A): 1.761185 object centre (A): 46.59150 35.64050 5.089500 number of atom coordinates read : 2379 total number of charged atoms : 2247 net assigned charge : -4.999986 assigned positive charge : 341.1185 centred at (gu) : 87.59070 91.53737 91.30651 assigned negative charge : -346.1187 centred at (gu) : 87.44577 91.52018 91.25521 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 60134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23245 grid for indexing accessible points = 1.400000 m= 18659 mr = 38978 m= 2188 mr = 12613 m= 81 mr = 1105 m= 0 mr = 15 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 542 time to turn everything in is 0.6000000 number of dielectric boundary points 28351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17535 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) : 0.5870616 object centre at (A) : 46.59150 35.64050 5.089500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6917601E-03 -4.8545385E-03 midg,1,midg; midg,igrid,midg -6.4228199E-02 6.7800572E-03 1,midg,midg; igrid,midg,midg -2.6527401E-03 1.3186064E-02 gauss-seidel spectral radius is 0.9983930 estimated iterations to convergence 198 setup time was (sec) 0.9800000 now iterating at: 17:02:33 rms-change max change #iterations 3.376032 184.3310 at 10iterations 1.481154 55.40509 at 20iterations 0.6494521 23.89935 at 30iterations 0.2822582 11.40126 at 40iterations 0.1240749 4.444596 at 50iterations 5.4372355E-02 1.948853 at 60iterations 2.3803554E-02 0.8193054 at 70iterations 1.0466843E-02 0.3803596 at 80iterations 4.5707296E-03 0.1640778 at 90iterations 2.0120766E-03 8.0730438E-02 at 100iterations 8.7720325E-04 3.3642292E-02 at 110iterations 3.8651418E-04 1.4060974E-02 at 120iterations finished qdiffx linear iterations at : 17:02:41 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 3.8651418E-04 1.4060974E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 17:02:43 9.701u 0.241s 0:10.91 91.1% 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 17:02:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 !!! WARNING: GLU 168 has a net charge of -2.0000 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: 2.641777 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): 17.51500 75.66800 ymin,ymax (A): 5.320000 65.96100 zmin,zma (A): -14.99500 25.17400 x,y,z range (A): 58.15300 60.64100 40.16900 scale (grids/A): 2.641777 object centre (A): 46.59150 35.64050 5.089500 number of atom coordinates read : 2379 total number of charged atoms : 2247 net assigned charge : -4.999986 assigned positive charge : 341.1185 centred at (gu) : 86.38605 92.30602 91.95964 assigned negative charge : -346.1187 centred at (gu) : 86.16875 92.28023 91.88278 start vw surface at 0.1800000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 139219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23245 grid for indexing accessible points = 1.400000 m= 63634 mr = 95752 m= 18729 mr = 49388 m= 3467 mr = 13811 m= 328 mr = 2339 m= 9 mr = 153 m= 0 mr = 4 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 1868 time to turn everything in is 1.370000 number of dielectric boundary points 63939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 17971 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) : 1.761185 object centre at (A) : 46.59150 35.64050 5.089500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5822975E-02 -5.2682530E-02 midg,1,midg; midg,igrid,midg -1.253912 -4.4422574E-02 1,midg,midg; igrid,midg,midg -9.9083409E-02 0.2218757 gauss-seidel spectral radius is 0.9991982 estimated iterations to convergence 279 setup time was (sec) 1.780000 now iterating at: 17:02:45 rms-change max change #iterations 8.435557 308.2016 at 10iterations 4.876962 164.1480 at 20iterations 2.787223 68.78558 at 30iterations 1.582899 40.26596 at 40iterations 0.8985665 21.39161 at 50iterations 0.5082046 10.88112 at 60iterations 0.2870552 6.225430 at 70iterations 0.1621459 3.413611 at 80iterations 9.1148540E-02 2.139938 at 90iterations 5.1176410E-02 1.151246 at 100iterations 2.8775213E-02 0.5928574 at 110iterations 1.6203525E-02 0.3342171 at 120iterations 9.1061527E-03 0.1935921 at 130iterations 5.1019625E-03 0.1243591 at 140iterations 2.8660190E-03 6.4819336E-02 at 150iterations 1.6087295E-03 3.6804199E-02 at 160iterations 9.0062729E-04 1.8831253E-02 at 170iterations 5.0610752E-04 1.0799408E-02 at 180iterations finished qdiffx linear iterations at : 17:02:57 total time elapsed so far: 14.06000 # loops : 180 mean,max change (kT/e) : 5.0610752E-04 1.0799408E-02 energy calculations done at 14.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.30000 DelPhi exited at 17:02:58 14.300u 0.246s 0:15.05 96.6% 0+0k 0+0io 0pf+0w