Sun Oct 9 00:36:34 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 Sun Oct 9 2011 at 00:36:34 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2322 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6442156 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): -26.96800 27.37900 ymin,ymax (A): 44.44100 86.17700 zmin,zma (A): -12.78700 42.47400 x,y,z range (A): 54.34700 41.73600 55.26100 scale (grids/A): 0.6442156 object centre (A): 0.2054996 65.30901 14.84350 number of atom coordinates read : 2322 total number of charged atoms : 2188 net assigned charge : 11.01402 assigned positive charge : 339.0116 centred at (gu) : 90.49029 91.10085 91.36710 assigned negative charge : -327.9982 centred at (gu) : 90.46310 91.01148 91.35658 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6753 nv = 96 ne = 84 npr = 46062 no. pairs analyzed = 46062 no. exposed pairs = 3073 no. arc points = 21911 no. surface atoms = 1027 nbur = 1295 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 3568 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2088 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2669185E-08 2.5271593E-08 midg,1,midg; midg,igrid,midg 6.4415979E-09 3.4833302E-08 1,midg,midg; igrid,midg,midg 1.3465550E-08 2.3092086E-08 gauss-seidel spectral radius is 0.9875011 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 00:36:34 rms-change max change #iterations 0.1416026 23.44355 at 10iterations 1.4073884E-02 2.188698 at 20iterations 1.4812804E-03 0.2030540 at 30iterations 1.8118665E-04 2.5627136E-02 at 40iterations 3.1137759E-05 5.0106049E-03 at 50iterations finished qdiffx linear iterations at : 00:36:37 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 3.1137759E-05 5.0106049E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 00:36:38 3.333u 0.182s 0:03.78 92.8% 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 Sun Oct 9 2011 at 00:36:38 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2322 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.932647 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): -26.96800 27.37900 ymin,ymax (A): 44.44100 86.17700 zmin,zma (A): -12.78700 42.47400 x,y,z range (A): 54.34700 41.73600 55.26100 scale (grids/A): 1.932647 object centre (A): 0.2054996 65.30901 14.84350 number of atom coordinates read : 2322 total number of charged atoms : 2188 net assigned charge : 11.01402 assigned positive charge : 339.0116 centred at (gu) : 91.47067 93.30255 94.10101 assigned negative charge : -327.9982 centred at (gu) : 91.38914 93.03450 94.06969 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71619 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21911 grid for indexing accessible points = 1.400000 m= 26386 mr = 48255 m= 4307 mr = 19128 m= 258 mr = 2596 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.3500000 number of dielectric boundary points 32502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17252 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) : 0.6442156 object centre at (A) : 0.2054996 65.30901 14.84350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4402014E-02 4.5402497E-02 midg,1,midg; midg,igrid,midg -4.0295981E-03 3.0622143E-02 1,midg,midg; igrid,midg,midg 4.2432852E-02 5.5095099E-02 gauss-seidel spectral radius is 0.9986559 estimated iterations to convergence 216 setup time was (sec) 0.5800000 now iterating at: 00:36:38 rms-change max change #iterations 4.008344 175.5892 at 10iterations 1.891917 78.77692 at 20iterations 0.8890213 28.18013 at 30iterations 0.4175359 12.93242 at 40iterations 0.1963540 6.465979 at 50iterations 9.2504509E-02 3.274364 at 60iterations 4.3561660E-02 1.438813 at 70iterations 2.0515110E-02 0.6433187 at 80iterations 9.6640270E-03 0.3498611 at 90iterations 4.5898124E-03 0.1363335 at 100iterations 2.1665737E-03 6.8367004E-02 at 110iterations 1.0385569E-03 3.4839630E-02 at 120iterations finished qdiffx linear iterations at : 00:36:45 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.0385569E-03 3.4839630E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 00:36:46 7.696u 0.171s 0:08.22 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 Sun Oct 9 2011 at 00:36:46 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2322 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.898970 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): -26.96800 27.37900 ymin,ymax (A): 44.44100 86.17700 zmin,zma (A): -12.78700 42.47400 x,y,z range (A): 54.34700 41.73600 55.26100 scale (grids/A): 2.898970 object centre (A): 0.2054996 65.30901 14.84350 number of atom coordinates read : 2322 total number of charged atoms : 2188 net assigned charge : 11.01402 assigned positive charge : 339.0116 centred at (gu) : 92.20606 94.95383 96.15147 assigned negative charge : -327.9982 centred at (gu) : 92.08384 94.55179 96.10460 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 165060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21911 grid for indexing accessible points = 1.400000 m= 84002 mr = 116818 m= 31491 mr = 67920 m= 7860 mr = 25048 m= 1149 mr = 5782 m= 68 mr = 749 m= 0 mr = 26 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1215 time to turn everything in is 0.9100000 number of dielectric boundary points 73287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 17500 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) : 1.932647 object centre at (A) : 0.2054996 65.30901 14.84350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.053150 0.5190862 midg,1,midg; midg,igrid,midg -3.9980859E-02 0.3052330 1,midg,midg; igrid,midg,midg 0.5125704 0.5871551 gauss-seidel spectral radius is 0.9992698 estimated iterations to convergence 292 setup time was (sec) 1.150000 now iterating at: 00:36:47 rms-change max change #iterations 9.493875 346.8937 at 10iterations 5.601711 131.4087 at 20iterations 3.289402 69.46306 at 30iterations 1.915634 38.86183 at 40iterations 1.117786 24.25931 at 50iterations 0.6491280 13.65262 at 60iterations 0.3776277 8.069649 at 70iterations 0.2192659 4.243076 at 80iterations 0.1272318 2.461069 at 90iterations 7.3666796E-02 1.502762 at 100iterations 4.2621203E-02 0.8260841 at 110iterations 2.4637548E-02 0.4587464 at 120iterations 1.4263060E-02 0.2714405 at 130iterations 8.2339738E-03 0.1685905 at 140iterations 4.7699315E-03 0.1037006 at 150iterations 2.7668942E-03 5.4012299E-02 at 160iterations 1.6074718E-03 2.9163361E-02 at 170iterations 9.3517062E-04 2.0057678E-02 at 180iterations finished qdiffx linear iterations at : 00:36:59 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 9.3517062E-04 2.0057678E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 00:36:59 12.477u 0.214s 0:12.96 97.8% 0+0k 0+0io 0pf+0w