Mon Oct 10 14:11:09 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 Mon Oct 10 2011 at 14:11:09 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5605152 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): -16.12600 34.56400 ymin,ymax (A): -25.87400 37.63900 zmin,zma (A): -3.847000 56.83500 x,y,z range (A): 50.69000 63.51300 60.68200 scale (grids/A): 0.5605152 object centre (A): 9.219002 5.882500 26.49400 number of atom coordinates read : 3182 total number of charged atoms : 3007 net assigned charge : 9.000011 assigned positive charge : 485.4539 centred at (gu) : 89.47981 90.45180 89.37655 assigned negative charge : -476.4551 centred at (gu) : 89.45091 90.53784 89.29027 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6680 nv = 96 ne = 84 npr = 61200 no. pairs analyzed = 61200 no. exposed pairs = 4397 no. arc points = 31882 no. surface atoms = 1456 nbur = 1726 mkacc time = 0.1800000 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 = 1.568000 m= 321 mr = 3257 m= 0 mr = 20 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3096 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8460 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2217420E-11 1.7426753E-09 midg,1,midg; midg,igrid,midg 1.8130234E-09 -7.3289465E-11 1,midg,midg; igrid,midg,midg 7.2126405E-10 1.1840371E-09 gauss-seidel spectral radius is 0.9836073 estimated iterations to convergence 64 setup time was (sec) 0.6500000 now iterating at: 14:11:10 rms-change max change #iterations 8.6946599E-02 14.62025 at 10iterations 6.2123435E-03 0.9869967 at 20iterations 4.5248997E-04 7.2671890E-02 at 30iterations 3.8114049E-05 6.4525604E-03 at 40iterations 5.3946324E-06 7.5697899E-04 at 50iterations finished qdiffx linear iterations at : 14:11:13 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 5.3946324E-06 7.5697899E-04 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 14:11:14 4.108u 0.259s 0:04.73 91.9% 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 14:11:14 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 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: 1.681545 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): -16.12600 34.56400 ymin,ymax (A): -25.87400 37.63900 zmin,zma (A): -3.847000 56.83500 x,y,z range (A): 50.69000 63.51300 60.68200 scale (grids/A): 1.681545 object centre (A): 9.219002 5.882500 26.49400 number of atom coordinates read : 3182 total number of charged atoms : 3007 net assigned charge : 9.000011 assigned positive charge : 485.4539 centred at (gu) : 88.43853 91.35458 88.12892 assigned negative charge : -476.4551 centred at (gu) : 88.35271 91.61288 87.87040 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31882 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22725 mr = 47723 m= 2528 mr = 15042 m= 91 mr = 1268 m= 0 mr = 10 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.6500000 number of dielectric boundary points 34439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 350 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23130 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) : 0.5605152 object centre at (A) : 9.219002 5.882500 26.49400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3232619E-05 1.9350972E-02 midg,1,midg; midg,igrid,midg 1.9937500E-02 1.6219590E-02 1,midg,midg; igrid,midg,midg 7.1786596E-03 5.1959469E-03 gauss-seidel spectral radius is 0.9983280 estimated iterations to convergence 194 setup time was (sec) 0.9500000 now iterating at: 14:11:15 rms-change max change #iterations 3.715942 157.4608 at 10iterations 1.593691 59.66467 at 20iterations 0.6883604 23.82134 at 30iterations 0.2963992 10.15849 at 40iterations 0.1278643 4.180333 at 50iterations 5.5356096E-02 1.841614 at 60iterations 2.3780076E-02 0.8655415 at 70iterations 1.0272401E-02 0.3532600 at 80iterations 4.4375183E-03 0.1577282 at 90iterations 1.9166771E-03 6.7794800E-02 at 100iterations 8.2595967E-04 3.1964302E-02 at 110iterations 3.5678301E-04 1.2413025E-02 at 120iterations finished qdiffx linear iterations at : 14:11:23 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 3.5678301E-04 1.2413025E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 14:11:24 9.460u 0.296s 0:10.06 96.9% 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 14:11:24 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.522318 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): -16.12600 34.56400 ymin,ymax (A): -25.87400 37.63900 zmin,zma (A): -3.847000 56.83500 x,y,z range (A): 50.69000 63.51300 60.68200 scale (grids/A): 2.522318 object centre (A): 9.219002 5.882500 26.49400 number of atom coordinates read : 3182 total number of charged atoms : 3007 net assigned charge : 9.000011 assigned positive charge : 485.4539 centred at (gu) : 87.65776 92.03156 87.19315 assigned negative charge : -476.4551 centred at (gu) : 87.52903 92.41915 86.80547 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 169539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31882 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77165 mr = 116924 m= 22649 mr = 59730 m= 4002 mr = 16534 m= 323 mr = 2576 m= 11 mr = 153 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 1.630000 number of dielectric boundary points 77773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 24039 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) : 1.681545 object centre at (A) : 9.219002 5.882500 26.49400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1152517 0.3191185 midg,1,midg; midg,igrid,midg 0.3357041 0.2403252 1,midg,midg; igrid,midg,midg 8.0190726E-02 3.7462175E-02 gauss-seidel spectral radius is 0.9991980 estimated iterations to convergence 279 setup time was (sec) 1.960000 now iterating at: 14:11:26 rms-change max change #iterations 9.662177 367.5956 at 10iterations 5.617009 176.4573 at 20iterations 3.247778 110.1667 at 30iterations 1.868020 65.70641 at 40iterations 1.066267 27.84761 at 50iterations 0.6089324 17.03201 at 60iterations 0.3448524 9.103725 at 70iterations 0.1953782 4.524929 at 80iterations 0.1105855 2.521893 at 90iterations 6.2524743E-02 1.689842 at 100iterations 3.5263304E-02 0.8171215 at 110iterations 1.9846749E-02 0.4071722 at 120iterations 1.1181285E-02 0.2393608 at 130iterations 6.3031078E-03 0.1280594 at 140iterations 3.5483884E-03 7.1119189E-02 at 150iterations 1.9958739E-03 4.6121597E-02 at 160iterations 1.1270706E-03 2.2745848E-02 at 170iterations 6.3663808E-04 1.2123108E-02 at 180iterations finished qdiffx linear iterations at : 14:11:40 total time elapsed so far: 15.74000 # loops : 180 mean,max change (kT/e) : 6.3663808E-04 1.2123108E-02 energy calculations done at 15.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 14:11:41 15.915u 0.295s 0:17.53 92.4% 0+0k 0+0io 0pf+0w