Tue Oct 11 06:44:13 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 06:44:13 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 = 2033 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6956929 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): -18.97500 23.83700 ymin,ymax (A): -12.31300 28.67300 zmin,zma (A): -3.136000 48.03600 x,y,z range (A): 42.81200 40.98600 51.17200 scale (grids/A): 0.6956929 object centre (A): 2.431000 8.180000 22.45000 number of atom coordinates read : 2033 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.71884 89.76188 90.41445 assigned negative charge : -304.2972 centred at (gu) : 89.54590 89.78124 90.43275 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6730 nv = 96 ne = 84 npr = 40158 no. pairs analyzed = 40158 no. exposed pairs = 2479 no. arc points = 17159 no. surface atoms = 848 nbur = 1185 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3828 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1613 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7518 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0558505E-08 4.4591300E-08 midg,1,midg; midg,igrid,midg 5.7726282E-08 3.9035129E-08 1,midg,midg; igrid,midg,midg -1.8213685E-08 1.0481659E-07 gauss-seidel spectral radius is 0.9892288 estimated iterations to convergence 78 setup time was (sec) 0.3400000 now iterating at: 06:44:13 rms-change max change #iterations 0.1837692 32.14137 at 10iterations 2.1710549E-02 2.936609 at 20iterations 2.8134277E-03 0.4208603 at 30iterations 4.5018509E-04 5.9250832E-02 at 40iterations 1.0449211E-04 1.2311935E-02 at 50iterations finished qdiffx linear iterations at : 06:44:16 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.0449211E-04 1.2311935E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:44:17 3.312u 0.170s 0:04.18 83.2% 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 Tue Oct 11 2011 at 06:44:17 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 = 2033 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.087079 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): -18.97500 23.83700 ymin,ymax (A): -12.31300 28.67300 zmin,zma (A): -3.136000 48.03600 x,y,z range (A): 42.81200 40.98600 51.17200 scale (grids/A): 2.087079 object centre (A): 2.431000 8.180000 22.45000 number of atom coordinates read : 2033 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.15662 89.28562 91.24327 assigned negative charge : -304.2972 centred at (gu) : 88.63786 89.34377 91.29861 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71448 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17159 grid for indexing accessible points = 1.400000 m= 28559 mr = 50713 m= 5368 mr = 21555 m= 457 mr = 3480 m= 6 mr = 226 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15300 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) : 0.6956929 object centre at (A) : 2.431000 8.180000 22.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3199435E-02 6.5960258E-02 midg,1,midg; midg,igrid,midg 2.5934113E-02 7.6582539E-03 1,midg,midg; igrid,midg,midg 8.6046364E-03 4.6414979E-02 gauss-seidel spectral radius is 0.9987914 estimated iterations to convergence 228 setup time was (sec) 0.5700000 now iterating at: 06:44:18 rms-change max change #iterations 4.396657 229.7214 at 10iterations 2.157263 77.16148 at 20iterations 1.055333 32.71907 at 30iterations 0.5207601 16.74820 at 40iterations 0.2547811 7.807032 at 50iterations 0.1255616 3.972467 at 60iterations 6.1554238E-02 2.168317 at 70iterations 3.0333884E-02 0.9190545 at 80iterations 1.4935713E-02 0.4725323 at 90iterations 7.3904009E-03 0.2731495 at 100iterations 3.6942193E-03 0.1122856 at 110iterations 1.8826895E-03 6.0653687E-02 at 120iterations finished qdiffx linear iterations at : 06:44:25 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.8826895E-03 6.0653687E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 06:44:25 7.723u 0.198s 0:08.38 94.3% 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 06:44:25 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 = 2033 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.130618 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): -18.97500 23.83700 ymin,ymax (A): -12.31300 28.67300 zmin,zma (A): -3.136000 48.03600 x,y,z range (A): 42.81200 40.98600 51.17200 scale (grids/A): 3.130618 object centre (A): 2.431000 8.180000 22.45000 number of atom coordinates read : 2033 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 88.73495 88.92835 91.86502 assigned negative charge : -304.2972 centred at (gu) : 87.95680 89.01569 91.94788 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 164570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17159 grid for indexing accessible points = 1.400000 m= 89484 mr = 122027 m= 35867 mr = 74268 m= 10093 mr = 29312 m= 1957 mr = 7777 m= 198 mr = 1421 m= 5 mr = 115 m= 0 mr = 2 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.090000 number of dielectric boundary points 67252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 15432 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) : 2.087079 object centre at (A) : 2.431000 8.180000 22.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3561797 0.7797513 midg,1,midg; midg,igrid,midg 0.2212101 4.3756146E-02 1,midg,midg; igrid,midg,midg 0.2329105 0.4017702 gauss-seidel spectral radius is 0.9992837 estimated iterations to convergence 295 setup time was (sec) 1.330000 now iterating at: 06:44:27 rms-change max change #iterations 9.892494 358.4640 at 10iterations 5.823997 132.1101 at 20iterations 3.432498 69.41248 at 30iterations 2.016678 44.60140 at 40iterations 1.180030 23.83877 at 50iterations 0.6907403 12.82944 at 60iterations 0.4040772 7.448045 at 70iterations 0.2358642 4.838592 at 80iterations 0.1375991 2.757980 at 90iterations 8.0451213E-02 1.353753 at 100iterations 4.7030181E-02 0.7958755 at 110iterations 2.7555645E-02 0.5115361 at 120iterations 1.6216068E-02 0.2858067 at 130iterations 9.6925450E-03 0.1825180 at 140iterations 5.8998037E-03 0.1082458 at 150iterations 3.7141030E-03 6.8981171E-02 at 160iterations 2.4654293E-03 5.0672531E-02 at 170iterations 1.7348531E-03 3.3710480E-02 at 180iterations finished qdiffx linear iterations at : 06:44:38 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 1.7348531E-03 3.3710480E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 06:44:38 12.438u 0.186s 0:12.99 97.0% 0+0k 0+0io 0pf+0w