Sat Oct 8 14:53:43 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 Sat Oct 8 2011 at 14:53:43 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 = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6388744 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): -12.16600 43.55700 ymin,ymax (A): -23.21100 22.50100 zmin,zma (A): -7.506000 47.12000 x,y,z range (A): 55.72300 45.71200 54.62600 scale (grids/A): 0.6388744 object centre (A): 15.69550 -0.3550005 19.80700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : -0.9999920 assigned positive charge : 453.0066 centred at (gu) : 88.84330 89.75628 91.76547 assigned negative charge : -454.0073 centred at (gu) : 88.80550 89.65872 91.71268 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8225 nv = 96 ne = 84 npr = 63413 no. pairs analyzed = 63413 no. exposed pairs = 3423 no. arc points = 24374 no. surface atoms = 1164 nbur = 1869 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 4828 m= 0 mr = 48 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2355 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10054 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7699507E-09 8.1396463E-09 midg,1,midg; midg,igrid,midg -1.5204934E-08 1.0692781E-08 1,midg,midg; igrid,midg,midg -8.2709848E-09 2.7281821E-09 gauss-seidel spectral radius is 0.9873395 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 14:53:44 rms-change max change #iterations 0.1541939 23.29322 at 10iterations 1.5578110E-02 2.385918 at 20iterations 1.5860872E-03 0.2079391 at 30iterations 1.8631051E-04 2.7904510E-02 at 40iterations 2.6220037E-05 3.9100647E-03 at 50iterations finished qdiffx linear iterations at : 14:53:47 total time elapsed so far: 4.120000 # loops : 50 mean,max change (kT/e) : 2.6220037E-05 3.9100647E-03 energy calculations done at 4.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 14:53:48 4.304u 0.246s 0:04.85 93.6% 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 Sat Oct 8 2011 at 14:53:48 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 = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.916623 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): -12.16600 43.55700 ymin,ymax (A): -23.21100 22.50100 zmin,zma (A): -7.506000 47.12000 x,y,z range (A): 55.72300 45.71200 54.62600 scale (grids/A): 1.916623 object centre (A): 15.69550 -0.3550005 19.80700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : -0.9999920 assigned positive charge : 453.0066 centred at (gu) : 86.52949 89.26809 95.29583 assigned negative charge : -454.0073 centred at (gu) : 86.41621 88.97585 95.13784 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24374 grid for indexing accessible points = 1.400000 m= 32335 mr = 64901 m= 4752 mr = 24349 m= 289 mr = 2950 m= 0 mr = 116 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 380 time to turn everything in is 0.6500000 number of dielectric boundary points 34811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 22745 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) : 0.6388744 object centre at (A) : 15.69550 -0.3550005 19.80700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8802166E-02 7.5139087E-03 midg,1,midg; midg,igrid,midg -9.6888776E-04 2.1394661E-02 1,midg,midg; igrid,midg,midg -3.4815952E-02 6.1978982E-03 gauss-seidel spectral radius is 0.9986869 estimated iterations to convergence 219 setup time was (sec) 0.9900000 now iterating at: 14:53:49 rms-change max change #iterations 4.697276 182.2716 at 10iterations 2.241725 71.91578 at 20iterations 1.067332 32.66521 at 30iterations 0.5066983 15.07056 at 40iterations 0.2415268 7.280479 at 50iterations 0.1148316 3.209984 at 60iterations 5.4760441E-02 1.564270 at 70iterations 2.6087584E-02 0.8650780 at 80iterations 1.2423301E-02 0.3603630 at 90iterations 5.9204814E-03 0.1754055 at 100iterations 2.8171840E-03 9.5342636E-02 at 110iterations 1.3448519E-03 4.1971207E-02 at 120iterations finished qdiffx linear iterations at : 14:53:58 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 1.3448519E-03 4.1971207E-02 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.920000 DelPhi exited at 14:53:58 9.919u 0.295s 0:10.48 97.3% 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 Sat Oct 8 2011 at 14:53:59 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 = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.874935 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): -12.16600 43.55700 ymin,ymax (A): -23.21100 22.50100 zmin,zma (A): -7.506000 47.12000 x,y,z range (A): 55.72300 45.71200 54.62600 scale (grids/A): 2.874935 object centre (A): 15.69550 -0.3550005 19.80700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : -0.9999920 assigned positive charge : 453.0066 centred at (gu) : 84.79400 88.90218 97.94352 assigned negative charge : -454.0073 centred at (gu) : 84.62437 88.46373 97.70675 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 207929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24374 grid for indexing accessible points = 1.400000 m= 106409 mr = 156697 m= 37162 mr = 88899 m= 8637 mr = 30063 m= 1279 mr = 6417 m= 62 mr = 849 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1198 time to turn everything in is 1.710000 number of dielectric boundary points 78530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 23084 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) : 1.916623 object centre at (A) : 15.69550 -0.3550005 19.80700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0325683E-02 0.2490041 midg,1,midg; midg,igrid,midg 4.1347137E-03 0.2579358 1,midg,midg; igrid,midg,midg -0.5428916 0.1460733 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 2.060000 now iterating at: 14:54:01 rms-change max change #iterations 10.89122 449.1959 at 10iterations 6.385445 125.0883 at 20iterations 3.722145 65.07689 at 30iterations 2.168320 37.35953 at 40iterations 1.258442 23.66513 at 50iterations 0.7313104 12.30075 at 60iterations 0.4247612 7.222160 at 70iterations 0.2459256 4.211746 at 80iterations 0.1425099 2.294682 at 90iterations 8.2553111E-02 1.519253 at 100iterations 4.7831751E-02 0.8566532 at 110iterations 2.7683405E-02 0.4562988 at 120iterations 1.6032478E-02 0.2672482 at 130iterations 9.2858663E-03 0.1540413 at 140iterations 5.3847772E-03 9.1405869E-02 at 150iterations 3.1201045E-03 5.3736210E-02 at 160iterations 1.8148187E-03 2.9947281E-02 at 170iterations 1.0603465E-03 1.8612862E-02 at 180iterations finished qdiffx linear iterations at : 14:54:15 total time elapsed so far: 16.02000 # loops : 180 mean,max change (kT/e) : 1.0603465E-03 1.8612862E-02 energy calculations done at 16.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.21000 DelPhi exited at 14:54:15 16.208u 0.308s 0:16.78 98.3% 0+0k 0+0io 0pf+0w