Sat Oct 15 13:42:17 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 13:42:17 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 = 2590 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: 0.6071873 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): -19.48900 39.14200 ymin,ymax (A): -26.37000 21.58000 zmin,zma (A): -12.04400 42.95400 x,y,z range (A): 58.63100 47.95000 54.99800 scale (grids/A): 0.6071873 object centre (A): 9.826501 -2.395000 15.45500 number of atom coordinates read : 2590 total number of charged atoms : 2440 net assigned charge : -8.499987 assigned positive charge : 384.3955 centred at (gu) : 90.04376 91.80029 91.10492 assigned negative charge : -392.8965 centred at (gu) : 89.91251 91.72071 90.99491 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6321 nv = 96 ne = 84 npr = 51891 no. pairs analyzed = 51891 no. exposed pairs = 3506 no. arc points = 24918 no. surface atoms = 1174 nbur = 1416 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3179 m= 0 mr = 26 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2900000 number of dielectric boundary points 3441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2435 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6729423E-09 4.3983409E-10 midg,1,midg; midg,igrid,midg -5.6389466E-09 -1.4948541E-09 1,midg,midg; igrid,midg,midg -1.0700336E-08 1.2437985E-09 gauss-seidel spectral radius is 0.9859644 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 13:42:18 rms-change max change #iterations 0.1128963 18.24770 at 10iterations 9.8521523E-03 1.599409 at 20iterations 8.5868320E-04 0.1555715 at 30iterations 7.9980768E-05 1.2247086E-02 at 40iterations 8.5078864E-06 1.5163422E-03 at 50iterations finished qdiffx linear iterations at : 13:42:22 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 8.5078864E-06 1.5163422E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 13:42:22 4.302u 0.251s 0:04.92 92.4% 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 13:42:22 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 = 2590 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: 1.821562 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): -19.48900 39.14200 ymin,ymax (A): -26.37000 21.58000 zmin,zma (A): -12.04400 42.95400 x,y,z range (A): 58.63100 47.95000 54.99800 scale (grids/A): 1.821562 object centre (A): 9.826501 -2.395000 15.45500 number of atom coordinates read : 2590 total number of charged atoms : 2440 net assigned charge : -8.499987 assigned positive charge : 384.3955 centred at (gu) : 90.13032 95.40025 93.31398 assigned negative charge : -392.8965 centred at (gu) : 89.73734 95.16183 92.98457 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24918 grid for indexing accessible points = 1.400000 m= 22304 mr = 45529 m= 3039 mr = 15263 m= 159 mr = 1693 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1174 time to turn everything in is 0.5300000 number of dielectric boundary points 31862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19142 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) : 0.6071873 object centre at (A) : 9.826501 -2.395000 15.45500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5793508E-02 -2.1108821E-02 midg,1,midg; midg,igrid,midg -1.1271426E-02 -9.0903826E-03 1,midg,midg; igrid,midg,midg 1.3526217E-03 -1.2265163E-02 gauss-seidel spectral radius is 0.9985191 estimated iterations to convergence 206 setup time was (sec) 0.8500000 now iterating at: 13:42:24 rms-change max change #iterations 3.893423 212.8370 at 10iterations 1.761695 62.85119 at 20iterations 0.7934737 27.26694 at 30iterations 0.3603572 11.76626 at 40iterations 0.1634642 5.765248 at 50iterations 7.3940925E-02 2.607938 at 60iterations 3.3519816E-02 1.064674 at 70iterations 1.5136875E-02 0.5124474 at 80iterations 6.8580708E-03 0.2313204 at 90iterations 3.1177730E-03 0.1093435 at 100iterations 1.4143275E-03 4.7856331E-02 at 110iterations 6.4168952E-04 2.0680904E-02 at 120iterations finished qdiffx linear iterations at : 13:42:32 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 6.4168952E-04 2.0680904E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.820000 DelPhi exited at 13:42:33 9.826u 0.327s 0:10.45 97.0% 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 Sat Oct 15 2011 at 13:42:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 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: 2.732343 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): -19.48900 39.14200 ymin,ymax (A): -26.37000 21.58000 zmin,zma (A): -12.04400 42.95400 x,y,z range (A): 58.63100 47.95000 54.99800 scale (grids/A): 2.732343 object centre (A): 9.826501 -2.395000 15.45500 number of atom coordinates read : 2590 total number of charged atoms : 2440 net assigned charge : -8.499987 assigned positive charge : 384.3955 centred at (gu) : 90.19524 98.09993 94.97083 assigned negative charge : -392.8965 centred at (gu) : 89.60598 97.74268 94.47684 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 159558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24918 grid for indexing accessible points = 1.400000 m= 74296 mr = 111515 m= 24152 mr = 58355 m= 5241 mr = 18240 m= 677 mr = 3618 m= 27 mr = 382 m= 0 mr = 5 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 3937 time to turn everything in is 1.340000 number of dielectric boundary points 71836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 19518 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) : 1.821562 object centre at (A) : 9.826501 -2.395000 15.45500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7513846E-02 -0.3575379 midg,1,midg; midg,igrid,midg -9.7020313E-02 -0.1152408 1,midg,midg; igrid,midg,midg 0.4985867 -0.1665488 gauss-seidel spectral radius is 0.9992344 estimated iterations to convergence 285 setup time was (sec) 1.680000 now iterating at: 13:42:35 rms-change max change #iterations 9.435468 294.5298 at 10iterations 5.474189 125.6864 at 20iterations 3.156890 63.62304 at 30iterations 1.806875 40.03837 at 40iterations 1.033295 20.85924 at 50iterations 0.5893013 12.86514 at 60iterations 0.3361906 7.562009 at 70iterations 0.1913106 3.967169 at 80iterations 0.1089674 1.937412 at 90iterations 6.2004145E-02 1.160523 at 100iterations 3.5262436E-02 0.7330475 at 110iterations 2.0015469E-02 0.4146314 at 120iterations 1.1381063E-02 0.2146864 at 130iterations 6.4751501E-03 0.1342468 at 140iterations 3.6787591E-03 7.4497223E-02 at 150iterations 2.0970043E-03 4.4561386E-02 at 160iterations 1.1942664E-03 2.2621155E-02 at 170iterations 6.8337994E-04 1.3276100E-02 at 180iterations finished qdiffx linear iterations at : 13:42:49 total time elapsed so far: 15.83000 # loops : 180 mean,max change (kT/e) : 6.8337994E-04 1.3276100E-02 energy calculations done at 15.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.01000 DelPhi exited at 13:42:50 16.011u 0.337s 0:16.77 97.4% 0+0k 0+0io 0pf+0w