Mon Oct 10 22:00:38 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 Mon Oct 10 2011 at 22:00:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5597748 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): -0.2490000 51.32100 ymin,ymax (A): -33.50500 23.48400 zmin,zma (A): -22.39600 41.20100 x,y,z range (A): 51.57000 56.98900 63.59700 scale (grids/A): 0.5597748 object centre (A): 25.53600 -5.010501 9.402500 number of atom coordinates read : 2855 total number of charged atoms : 2779 net assigned charge : 1.500009 assigned positive charge : 421.9531 centred at (gu) : 88.06410 89.10706 89.29538 assigned negative charge : -420.4546 centred at (gu) : 88.13182 89.17736 89.39502 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6074 nv = 96 ne = 84 npr = 55372 no. pairs analyzed = 55372 no. exposed pairs = 3885 no. arc points = 27882 no. surface atoms = 1304 nbur = 1551 mkacc time = 0.1200000 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 = 1.540000 m= 273 mr = 2989 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2910 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7939 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3618426E-09 -7.6918361E-10 midg,1,midg; midg,igrid,midg 1.0560559E-09 -4.8542464E-10 1,midg,midg; igrid,midg,midg 1.3256988E-09 -3.5896480E-10 gauss-seidel spectral radius is 0.9835430 estimated iterations to convergence 64 setup time was (sec) 0.5200000 now iterating at: 22:00:38 rms-change max change #iterations 7.6914072E-02 12.78052 at 10iterations 5.5853557E-03 0.9427700 at 20iterations 4.3708488E-04 7.4177742E-02 at 30iterations 5.0832037E-05 7.5225830E-03 at 40iterations 9.1166639E-06 1.1997223E-03 at 50iterations finished qdiffx linear iterations at : 22:00:41 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 9.1166639E-06 1.1997223E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 22:00:42 3.274u 0.153s 0:03.94 86.8% 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 Mon Oct 10 2011 at 22:00:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.679325 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): -0.2490000 51.32100 ymin,ymax (A): -33.50500 23.48400 zmin,zma (A): -22.39600 41.20100 x,y,z range (A): 51.57000 56.98900 63.59700 scale (grids/A): 1.679325 object centre (A): 25.53600 -5.010501 9.402500 number of atom coordinates read : 2855 total number of charged atoms : 2779 net assigned charge : 1.500009 assigned positive charge : 421.9531 centred at (gu) : 84.19125 87.32018 87.88557 assigned negative charge : -420.4546 centred at (gu) : 84.39536 87.53183 88.18490 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27882 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20297 mr = 43773 m= 2332 mr = 13541 m= 74 mr = 1171 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 31168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 21495 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) : 0.5597748 object centre at (A) : 25.53600 -5.010501 9.402500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1563218E-02 -2.4110466E-02 midg,1,midg; midg,igrid,midg 2.1985355E-03 -1.1707918E-02 1,midg,midg; igrid,midg,midg 2.0761915E-02 3.5061724E-03 gauss-seidel spectral radius is 0.9982891 estimated iterations to convergence 192 setup time was (sec) 0.7800000 now iterating at: 22:00:43 rms-change max change #iterations 3.410312 174.0375 at 10iterations 1.442638 54.09879 at 20iterations 0.6188579 26.34086 at 30iterations 0.2631809 9.079109 at 40iterations 0.1120607 4.087198 at 50iterations 4.7948238E-02 1.775737 at 60iterations 2.0495096E-02 0.7463365 at 70iterations 8.7398812E-03 0.3382492 at 80iterations 3.7542304E-03 0.1329889 at 90iterations 1.6015669E-03 5.5430770E-02 at 100iterations 6.8663276E-04 2.7482986E-02 at 110iterations 2.9629486E-04 1.0072708E-02 at 120iterations finished qdiffx linear iterations at : 22:00:49 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 2.9629486E-04 1.0072708E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 22:00:50 7.379u 0.215s 0:08.13 93.2% 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 Mon Oct 10 2011 at 22:00:50 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 = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.518987 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): -0.2490000 51.32100 ymin,ymax (A): -33.50500 23.48400 zmin,zma (A): -22.39600 41.20100 x,y,z range (A): 51.57000 56.98900 63.59700 scale (grids/A): 2.518987 object centre (A): 25.53600 -5.010501 9.402500 number of atom coordinates read : 2855 total number of charged atoms : 2779 net assigned charge : 1.500009 assigned positive charge : 421.9531 centred at (gu) : 81.28664 85.98002 86.82809 assigned negative charge : -420.4546 centred at (gu) : 81.59299 86.29768 87.27743 start vw surface at 0.1900000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 155577 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27882 grid for indexing accessible points = 1.400000 m= 69092 mr = 107762 m= 20699 mr = 53289 m= 3571 mr = 15290 m= 281 mr = 2419 m= 5 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 70338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 22218 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) : 1.679325 object centre at (A) : 25.53600 -5.010501 9.402500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2094340 -0.5927219 midg,1,midg; midg,igrid,midg 4.4506374E-03 -0.1542105 1,midg,midg; igrid,midg,midg 0.2557176 6.6959850E-02 gauss-seidel spectral radius is 0.9991737 estimated iterations to convergence 275 setup time was (sec) 1.470000 now iterating at: 22:00:52 rms-change max change #iterations 8.718858 329.5024 at 10iterations 4.986797 120.1173 at 20iterations 2.834489 66.63165 at 30iterations 1.602619 37.08099 at 40iterations 0.9027097 18.04029 at 50iterations 0.5082187 11.04285 at 60iterations 0.2843716 5.873400 at 70iterations 0.1591866 3.815971 at 80iterations 8.8700660E-02 1.983416 at 90iterations 4.9649917E-02 1.034589 at 100iterations 2.7675498E-02 0.5836267 at 110iterations 1.5429849E-02 0.3451920 at 120iterations 8.6011821E-03 0.1774125 at 130iterations 4.7881934E-03 0.1042557 at 140iterations 2.6700252E-03 5.7001114E-02 at 150iterations 1.4859105E-03 2.9496670E-02 at 160iterations 8.3140907E-04 1.6552448E-02 at 170iterations 4.6454286E-04 9.4804764E-03 at 180iterations finished qdiffx linear iterations at : 22:01:02 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 4.6454286E-04 9.4804764E-03 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 22:01:03 11.909u 0.235s 0:12.83 94.5% 0+0k 0+0io 0pf+0w