Sat Oct 15 13:13:36 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 13:13:37 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3306 !!! WARNING: LLP 1 has a net charge of 1.5300 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: 0.5731674 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): -11.19800 50.91300 ymin,ymax (A): -13.10900 42.47000 zmin,zma (A): 20.26300 75.71100 x,y,z range (A): 62.11100 55.57899 55.44800 scale (grids/A): 0.5731674 object centre (A): 19.85750 14.68050 47.98700 number of atom coordinates read : 3306 total number of charged atoms : 3150 net assigned charge : 5.030017 assigned positive charge : 509.2396 centred at (gu) : 90.93831 89.92451 87.75919 assigned negative charge : -504.2111 centred at (gu) : 90.81480 90.04414 87.75645 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7228 nv = 96 ne = 84 npr = 64320 no. pairs analyzed = 64320 no. exposed pairs = 4421 no. arc points = 30826 no. surface atoms = 1488 nbur = 1818 mkacc time = 0.1100000 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= 356 mr = 3624 m= 1 mr = 32 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 0.2300000 number of dielectric boundary points 3929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3000 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9072 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3110224E-09 5.3494981E-10 midg,1,midg; midg,igrid,midg 3.2179717E-09 -1.5298712E-09 1,midg,midg; igrid,midg,midg -1.3000192E-09 4.0487116E-09 gauss-seidel spectral radius is 0.9843227 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 13:13:39 rms-change max change #iterations 9.7021371E-02 18.37579 at 10iterations 7.2933421E-03 0.9801302 at 20iterations 5.5754185E-04 8.4398270E-02 at 30iterations 5.3350344E-05 7.4019432E-03 at 40iterations 1.7641085E-05 2.4976730E-03 at 50iterations finished qdiffx linear iterations at : 13:13:44 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.7641085E-05 2.4976730E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 13:13:44 3.422u 0.175s 0:07.94 45.2% 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 Sat Oct 15 2011 at 13:13:45 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3306 !!! WARNING: LLP 1 has a net charge of 1.5300 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: 1.719502 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): -11.19800 50.91300 ymin,ymax (A): -13.10900 42.47000 zmin,zma (A): 20.26300 75.71100 x,y,z range (A): 62.11100 55.57899 55.44800 scale (grids/A): 1.719502 object centre (A): 19.85750 14.68050 47.98700 number of atom coordinates read : 3306 total number of charged atoms : 3150 net assigned charge : 5.030017 assigned positive charge : 509.2396 centred at (gu) : 92.81409 89.77255 83.27696 assigned negative charge : -504.2111 centred at (gu) : 92.44394 90.13221 83.26911 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30826 grid for indexing accessible points = 1.400000 m= 26576 mr = 53354 m= 3556 mr = 17979 m= 148 mr = 1874 m= 0 mr = 25 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 36510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 24376 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) : 0.5731674 object centre at (A) : 19.85750 14.68050 47.98700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2040265E-02 5.7017389E-03 midg,1,midg; midg,igrid,midg 2.5526265E-02 -9.5975017E-03 1,midg,midg; igrid,midg,midg -9.0289190E-03 1.8730402E-02 gauss-seidel spectral radius is 0.9984053 estimated iterations to convergence 199 setup time was (sec) 0.6800000 now iterating at: 13:13:46 rms-change max change #iterations 4.035752 178.6528 at 10iterations 1.775326 64.47170 at 20iterations 0.7870500 25.26956 at 30iterations 0.3467461 12.32719 at 40iterations 0.1538426 5.314608 at 50iterations 6.7756236E-02 2.558711 at 60iterations 2.9883152E-02 1.121182 at 70iterations 1.3260504E-02 0.4436722 at 80iterations 5.8608693E-03 0.1998329 at 90iterations 2.5977138E-03 8.3114147E-02 at 100iterations 1.1531321E-03 3.7462234E-02 at 110iterations 5.2754133E-04 1.8323898E-02 at 120iterations finished qdiffx linear iterations at : 13:13:54 total time elapsed so far: 8.770000 # loops : 120 mean,max change (kT/e) : 5.2754133E-04 1.8323898E-02 energy calculations done at 8.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.900000 DelPhi exited at 13:13:54 8.902u 0.287s 0:09.60 95.6% 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 13:13:54 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3306 !!! WARNING: LLP 1 has a net charge of 1.5300 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: 2.579253 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): -11.19800 50.91300 ymin,ymax (A): -13.10900 42.47000 zmin,zma (A): 20.26300 75.71100 x,y,z range (A): 62.11100 55.57899 55.44800 scale (grids/A): 2.579253 object centre (A): 19.85750 14.68050 47.98700 number of atom coordinates read : 3306 total number of charged atoms : 3150 net assigned charge : 5.030017 assigned positive charge : 509.2396 centred at (gu) : 94.22115 89.65837 79.91514 assigned negative charge : -504.2111 centred at (gu) : 93.66592 90.19798 79.90356 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 184162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30826 grid for indexing accessible points = 1.400000 m= 88392 mr = 130711 m= 28678 mr = 69099 m= 5936 mr = 21330 m= 624 mr = 3957 m= 26 mr = 350 m= 0 mr = 7 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 82364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 25164 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) : 1.719502 object centre at (A) : 19.85750 14.68050 47.98700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3305371 6.8687677E-02 midg,1,midg; midg,igrid,midg 0.3795331 -0.1079820 1,midg,midg; igrid,midg,midg 0.1218024 0.2184647 gauss-seidel spectral radius is 0.9992194 estimated iterations to convergence 283 setup time was (sec) 1.200000 now iterating at: 13:13:57 rms-change max change #iterations 10.38053 343.3259 at 10iterations 6.127592 177.0872 at 20iterations 3.582282 77.67928 at 30iterations 2.072809 46.22178 at 40iterations 1.194863 26.98801 at 50iterations 0.6857659 15.32190 at 60iterations 0.3927677 7.647003 at 70iterations 0.2245651 4.710267 at 80iterations 0.1281367 2.625359 at 90iterations 7.3068865E-02 1.383665 at 100iterations 4.1634411E-02 0.8701038 at 110iterations 2.3729598E-02 0.5173950 at 120iterations 1.3558385E-02 0.2843952 at 130iterations 7.7431835E-03 0.1494064 at 140iterations 4.4835480E-03 9.1323495E-02 at 150iterations 2.6498579E-03 5.3932190E-02 at 160iterations 1.6436273E-03 3.3246368E-02 at 170iterations 1.0997481E-03 2.2256851E-02 at 180iterations finished qdiffx linear iterations at : 13:14:10 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.0997481E-03 2.2256851E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 13:14:11 12.895u 0.229s 0:16.37 80.0% 0+0k 0+0io 0pf+0w