Tue Oct 11 03:16:51 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 Tue Oct 11 2011 at 03:16:51 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 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: 0.6823584 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): -10.02700 41.11700 ymin,ymax (A): 3.401000 55.57300 zmin,zma (A): 104.8340 149.6850 x,y,z range (A): 51.14400 52.17200 44.85100 scale (grids/A): 0.6823584 object centre (A): 15.54500 29.48700 127.2595 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 2.500013 assigned positive charge : 394.3917 centred at (gu) : 89.41385 90.97852 88.79457 assigned negative charge : -391.8926 centred at (gu) : 89.27834 91.05013 89.02963 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8150 nv = 96 ne = 84 npr = 52172 no. pairs analyzed = 52172 no. exposed pairs = 3219 no. arc points = 22474 no. surface atoms = 1090 nbur = 1474 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 530 mr = 4544 m= 4 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1616368E-07 -5.6532354E-08 midg,1,midg; midg,igrid,midg 2.9298754E-08 -1.7334918E-08 1,midg,midg; igrid,midg,midg -4.1487876E-08 5.0938038E-08 gauss-seidel spectral radius is 0.9888654 estimated iterations to convergence 77 setup time was (sec) 0.5600000 now iterating at: 03:16:52 rms-change max change #iterations 0.1910449 26.22340 at 10iterations 2.2382226E-02 2.888470 at 20iterations 2.7469469E-03 0.3292274 at 30iterations 4.0834589E-04 5.4134369E-02 at 40iterations 8.2829843E-05 1.0833740E-02 at 50iterations finished qdiffx linear iterations at : 03:16:56 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 8.2829843E-05 1.0833740E-02 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 03:16:57 4.573u 0.408s 0:05.65 87.9% 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 Tue Oct 11 2011 at 03:16:57 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 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: 2.047075 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): -10.02700 41.11700 ymin,ymax (A): 3.401000 55.57300 zmin,zma (A): 104.8340 149.6850 x,y,z range (A): 51.14400 52.17200 44.85100 scale (grids/A): 2.047075 object centre (A): 15.54500 29.48700 127.2595 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 2.500013 assigned positive charge : 394.3917 centred at (gu) : 88.24083 92.93501 86.38297 assigned negative charge : -391.8926 centred at (gu) : 87.83463 93.15026 87.08870 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22474 grid for indexing accessible points = 1.400000 m= 33566 mr = 59952 m= 6599 mr = 25284 m= 500 mr = 4310 m= 11 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 37299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 19261 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) : 0.6823584 object centre at (A) : 15.54500 29.48700 127.2595 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6221667E-02 -3.8440432E-02 midg,1,midg; midg,igrid,midg 1.7641451E-02 -1.4188661E-02 1,midg,midg; igrid,midg,midg -1.7890535E-02 4.0650573E-02 gauss-seidel spectral radius is 0.9988129 estimated iterations to convergence 230 setup time was (sec) 1.030000 now iterating at: 03:16:58 rms-change max change #iterations 4.996520 203.7995 at 10iterations 2.465281 76.02137 at 20iterations 1.221170 36.93425 at 30iterations 0.6025716 17.96768 at 40iterations 0.2982198 8.627537 at 50iterations 0.1473713 4.755432 at 60iterations 7.2579384E-02 2.183897 at 70iterations 3.5852298E-02 1.042633 at 80iterations 1.7765753E-02 0.5400539 at 90iterations 8.8188043E-03 0.2589226 at 100iterations 4.3499512E-03 0.1169891 at 110iterations 2.1523610E-03 5.9890747E-02 at 120iterations finished qdiffx linear iterations at : 03:17:09 total time elapsed so far: 11.20000 # loops : 120 mean,max change (kT/e) : 2.1523610E-03 5.9890747E-02 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 03:17:09 11.369u 0.417s 0:12.44 94.6% 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 03:17:10 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 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: 3.070613 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): -10.02700 41.11700 ymin,ymax (A): 3.401000 55.57300 zmin,zma (A): 104.8340 149.6850 x,y,z range (A): 51.14400 52.17200 44.85100 scale (grids/A): 3.070613 object centre (A): 15.54500 29.48700 127.2595 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 2.500013 assigned positive charge : 394.3917 centred at (gu) : 87.36121 94.40233 84.57426 assigned negative charge : -391.8926 centred at (gu) : 86.75185 94.72540 85.63305 start vw surface at 0.1100000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 199571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22474 grid for indexing accessible points = 1.400000 m= 104765 mr = 145226 m= 42715 mr = 86066 m= 12257 mr = 35132 m= 2217 mr = 9515 m= 192 mr = 1534 m= 4 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.970000 number of dielectric boundary points 84148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 19456 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) : 2.047075 object centre at (A) : 15.54500 29.48700 127.2595 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8673447 -0.3777634 midg,1,midg; midg,igrid,midg 0.1443358 -0.2034884 1,midg,midg; igrid,midg,midg -7.6625250E-02 0.4761391 gauss-seidel spectral radius is 0.9993073 estimated iterations to convergence 300 setup time was (sec) 2.300000 now iterating at: 03:17:12 rms-change max change #iterations 11.29584 412.0142 at 10iterations 6.693519 132.2509 at 20iterations 3.953528 75.37344 at 30iterations 2.337644 40.97020 at 40iterations 1.376437 22.69563 at 50iterations 0.8106567 13.45692 at 60iterations 0.4753297 7.891495 at 70iterations 0.2796324 4.818384 at 80iterations 0.1640863 2.887681 at 90iterations 9.6365392E-02 1.636158 at 100iterations 5.6400150E-02 0.9530487 at 110iterations 3.3119593E-02 0.5862331 at 120iterations 1.9428523E-02 0.3027878 at 130iterations 1.1407332E-02 0.1845284 at 140iterations 6.7089251E-03 0.1180439 at 150iterations 3.9601615E-03 6.8086624E-02 at 160iterations 2.3504205E-03 3.8679063E-02 at 170iterations 1.4048746E-03 2.5944710E-02 at 180iterations finished qdiffx linear iterations at : 03:17:30 total time elapsed so far: 19.57000 # loops : 180 mean,max change (kT/e) : 1.4048746E-03 2.5944710E-02 energy calculations done at 19.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.74000 DelPhi exited at 03:17:30 19.747u 0.475s 0:20.53 98.4% 0+0k 0+0io 0pf+0w