Sun Oct 9 06:12:31 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 Sun Oct 9 2011 at 06:12:31 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.6598948 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): 2.055000 44.33600 ymin,ymax (A): -8.868000 38.14500 zmin,zma (A): -24.20500 29.74300 x,y,z range (A): 42.28100 47.01300 53.94800 scale (grids/A): 0.6598948 object centre (A): 23.19550 14.63850 2.769000 number of atom coordinates read : 1997 total number of charged atoms : 1858 net assigned charge : -2.499985 assigned positive charge : 298.8951 centred at (gu) : 89.96967 89.11375 88.06985 assigned negative charge : -301.3951 centred at (gu) : 89.80196 88.93306 88.02563 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5844 nv = 96 ne = 84 npr = 42049 no. pairs analyzed = 42049 no. exposed pairs = 2440 no. arc points = 17479 no. surface atoms = 814 nbur = 1183 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3237 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2500000 number of dielectric boundary points 2866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1662 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6792 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8858003E-08 4.9438958E-10 midg,1,midg; midg,igrid,midg -4.0893632E-08 1.7525414E-08 1,midg,midg; igrid,midg,midg -3.2052849E-08 1.9161849E-08 gauss-seidel spectral radius is 0.9880416 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 06:12:32 rms-change max change #iterations 0.1507608 25.90106 at 10iterations 1.5864436E-02 2.505169 at 20iterations 1.6642060E-03 0.2396164 at 30iterations 1.7875557E-04 2.8144836E-02 at 40iterations 1.8604698E-05 2.8247833E-03 at 50iterations finished qdiffx linear iterations at : 06:12:34 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.8604698E-05 2.8247833E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 06:12:35 3.121u 0.165s 0:03.56 92.1% 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 Sun Oct 9 2011 at 06:12:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 1.979684 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): 2.055000 44.33600 ymin,ymax (A): -8.868000 38.14500 zmin,zma (A): -24.20500 29.74300 x,y,z range (A): 42.28100 47.01300 53.94800 scale (grids/A): 1.979684 object centre (A): 23.19550 14.63850 2.769000 number of atom coordinates read : 1997 total number of charged atoms : 1858 net assigned charge : -2.499985 assigned positive charge : 298.8951 centred at (gu) : 89.90916 87.34134 84.20969 assigned negative charge : -301.3951 centred at (gu) : 89.40575 86.79931 84.07709 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17479 grid for indexing accessible points = 1.400000 m= 23284 mr = 42833 m= 4101 mr = 17604 m= 285 mr = 2800 m= 5 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2650 time to turn everything in is 0.4500000 number of dielectric boundary points 26401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14680 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) : 0.6598948 object centre at (A) : 23.19550 14.63850 2.769000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9888793E-02 2.4180619E-02 midg,1,midg; midg,igrid,midg -2.5707878E-02 1.4119955E-02 1,midg,midg; igrid,midg,midg -3.4221329E-02 8.4780389E-03 gauss-seidel spectral radius is 0.9986671 estimated iterations to convergence 217 setup time was (sec) 0.7300000 now iterating at: 06:12:36 rms-change max change #iterations 4.047456 215.3162 at 10iterations 1.903202 74.04877 at 20iterations 0.8952397 28.85026 at 30iterations 0.4245586 14.12303 at 40iterations 0.2001758 6.847506 at 50iterations 9.4554298E-02 3.042407 at 60iterations 4.4757474E-02 1.557770 at 70iterations 2.1053895E-02 0.6555405 at 80iterations 9.9613946E-03 0.3216343 at 90iterations 4.7203950E-03 0.1584282 at 100iterations 2.2322503E-03 8.1216812E-02 at 110iterations 1.0544041E-03 3.8599014E-02 at 120iterations finished qdiffx linear iterations at : 06:12:42 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 1.0544041E-03 3.8599014E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 06:12:42 7.008u 0.211s 0:07.49 96.2% 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 Sun Oct 9 2011 at 06:12:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.969526 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): 2.055000 44.33600 ymin,ymax (A): -8.868000 38.14500 zmin,zma (A): -24.20500 29.74300 x,y,z range (A): 42.28100 47.01300 53.94800 scale (grids/A): 2.969526 object centre (A): 23.19550 14.63850 2.769000 number of atom coordinates read : 1997 total number of charged atoms : 1858 net assigned charge : -2.499985 assigned positive charge : 298.8951 centred at (gu) : 89.86372 86.01202 81.31457 assigned negative charge : -301.3951 centred at (gu) : 89.10863 85.19906 81.11562 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 143233 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17479 grid for indexing accessible points = 1.400000 m= 73487 mr = 103127 m= 28381 mr = 60939 m= 7675 mr = 23563 m= 1316 mr = 6073 m= 86 mr = 922 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 8965 time to turn everything in is 1.120000 number of dielectric boundary points 59517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 14864 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) : 1.979684 object centre at (A) : 23.19550 14.63850 2.769000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6532068 0.6125317 midg,1,midg; midg,igrid,midg -0.1759886 0.1859349 1,midg,midg; igrid,midg,midg -0.3375768 3.7343208E-02 gauss-seidel spectral radius is 0.9992517 estimated iterations to convergence 289 setup time was (sec) 1.410000 now iterating at: 06:12:44 rms-change max change #iterations 9.267837 430.1877 at 10iterations 5.327895 154.4634 at 20iterations 3.055352 72.10850 at 30iterations 1.753969 38.15811 at 40iterations 1.007688 21.30550 at 50iterations 0.5791038 12.02020 at 60iterations 0.3307020 7.386879 at 70iterations 0.1895750 4.014410 at 80iterations 0.1083363 2.080043 at 90iterations 6.2259577E-02 1.345474 at 100iterations 3.5552997E-02 0.7770844 at 110iterations 2.0319799E-02 0.3742466 at 120iterations 1.1649636E-02 0.2328641 at 130iterations 6.6574188E-03 0.1252041 at 140iterations 3.8173939E-03 9.2937469E-02 at 150iterations 2.1845838E-03 4.5168877E-02 at 160iterations 1.2486406E-03 2.3406982E-02 at 170iterations 7.1665819E-04 1.3427734E-02 at 180iterations finished qdiffx linear iterations at : 06:12:54 total time elapsed so far: 11.08000 # loops : 180 mean,max change (kT/e) : 7.1665819E-04 1.3427734E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 06:12:54 11.251u 0.271s 0:11.81 97.5% 0+0k 0+0io 0pf+0w