Tue Oct 11 08:20:22 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 Tue Oct 11 2011 at 08:20:22 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5885465 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 0.5885465 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3744 total number of charged atoms : 3622 net assigned charge : -2.499984 assigned positive charge : 570.6261 centred at (gu) : 90.31406 89.83324 90.58729 assigned negative charge : -573.1282 centred at (gu) : 90.17425 89.82511 90.52110 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8359 nv = 96 ne = 84 npr = 76955 no. pairs analyzed = 76955 no. exposed pairs = 4276 no. arc points = 29728 no. surface atoms = 1449 nbur = 2295 mkacc time = 0.1600000 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 = 1.456000 m= 390 mr = 4706 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3800000 number of dielectric boundary points 4012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3093 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10871 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8511484E-09 1.9629987E-09 midg,1,midg; midg,igrid,midg -1.1089875E-09 -4.4143203E-10 1,midg,midg; igrid,midg,midg -5.6675806E-09 4.7426516E-09 gauss-seidel spectral radius is 0.9851540 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 08:20:23 rms-change max change #iterations 0.1240617 16.99315 at 10iterations 1.0106102E-02 1.390071 at 20iterations 8.3027279E-04 0.1172409 at 30iterations 6.9009577E-05 1.0503769E-02 at 40iterations 6.1126766E-06 8.3160400E-04 at 50iterations finished qdiffx linear iterations at : 08:20:26 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 6.1126766E-06 8.3160400E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:20:26 3.384u 0.190s 0:03.98 89.6% 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 Tue Oct 11 2011 at 08:20:26 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3744 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: 1.765640 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 1.765640 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3744 total number of charged atoms : 3622 net assigned charge : -2.499984 assigned positive charge : 570.6261 centred at (gu) : 90.94061 89.49849 91.76066 assigned negative charge : -573.1282 centred at (gu) : 90.52200 89.47466 91.56281 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 93466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29728 grid for indexing accessible points = 1.400000 m= 30520 mr = 66506 m= 3786 mr = 22331 m= 146 mr = 2225 m= 0 mr = 37 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3656 time to turn everything in is 0.6000000 number of dielectric boundary points 36819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 253 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 28173 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) : 0.5885465 object centre at (A) : 45.21700 -19.35900 103.6005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6852193E-03 2.6395418E-02 midg,1,midg; midg,igrid,midg -3.9666602E-03 1.9548724E-03 1,midg,midg; igrid,midg,midg -3.5375033E-02 5.1500346E-04 gauss-seidel spectral radius is 0.9985220 estimated iterations to convergence 206 setup time was (sec) 0.8600000 now iterating at: 08:20:27 rms-change max change #iterations 4.546930 180.4439 at 10iterations 2.065356 66.68272 at 20iterations 0.9390407 28.48391 at 30iterations 0.4267316 13.31136 at 40iterations 0.1939476 5.308231 at 50iterations 8.7958649E-02 2.548009 at 60iterations 3.9970707E-02 1.191993 at 70iterations 1.8172542E-02 0.5012994 at 80iterations 8.2885409E-03 0.2305698 at 90iterations 3.7593895E-03 0.1056557 at 100iterations 1.7109544E-03 4.9267769E-02 at 110iterations 7.7808340E-04 2.2953510E-02 at 120iterations finished qdiffx linear iterations at : 08:20:33 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 7.7808340E-04 2.2953510E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 08:20:34 7.216u 0.187s 0:07.79 94.8% 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 Tue Oct 11 2011 at 08:20:34 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.648459 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 2.648459 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3744 total number of charged atoms : 3622 net assigned charge : -2.499984 assigned positive charge : 570.6261 centred at (gu) : 91.41074 89.24749 92.64063 assigned negative charge : -573.1282 centred at (gu) : 90.78291 89.21193 92.34427 start vw surface at 0.2400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 217282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29728 grid for indexing accessible points = 1.400000 m= 104326 mr = 161743 m= 32718 mr = 85676 m= 6484 mr = 25893 m= 625 mr = 4714 m= 19 mr = 354 m= 0 mr = 6 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 12273 time to turn everything in is 1.620000 number of dielectric boundary points 83068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 28969 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) : 1.765640 object centre at (A) : 45.21700 -19.35900 103.6005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1208645 0.4107445 midg,1,midg; midg,igrid,midg -3.3724420E-03 -7.7509563E-03 1,midg,midg; igrid,midg,midg -0.4935070 -0.1919415 gauss-seidel spectral radius is 0.9992511 estimated iterations to convergence 288 setup time was (sec) 1.910000 now iterating at: 08:20:36 rms-change max change #iterations 11.01453 290.6702 at 10iterations 6.412190 149.9254 at 20iterations 3.699081 75.17924 at 30iterations 2.133710 48.79653 at 40iterations 1.228332 25.00392 at 50iterations 0.7047112 11.74535 at 60iterations 0.4046171 7.913884 at 70iterations 0.2317441 4.073456 at 80iterations 0.1329554 2.581207 at 90iterations 7.5936437E-02 1.328051 at 100iterations 4.3584190E-02 0.7317848 at 110iterations 2.4924429E-02 0.4298158 at 120iterations 1.4258441E-02 0.2423401 at 130iterations 8.1698196E-03 0.1338415 at 140iterations 4.6739103E-03 7.9055786E-02 at 150iterations 2.6752066E-03 4.4372559E-02 at 160iterations 1.5310667E-03 2.6111603E-02 at 170iterations 8.7738421E-04 1.4310837E-02 at 180iterations finished qdiffx linear iterations at : 08:20:46 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 8.7738421E-04 1.4310837E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 08:20:47 12.379u 0.178s 0:13.21 94.9% 0+0k 0+0io 0pf+0w