Sat Oct 8 16:47:05 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 16:47:05 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 = 4441 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5463895 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): 15.68100 78.81600 ymin,ymax (A): 120.1650 185.3200 zmin,zma (A): -1.378000 60.16200 x,y,z range (A): 63.13500 65.15499 61.54000 scale (grids/A): 0.5463895 object centre (A): 47.24850 152.7425 29.39200 number of atom coordinates read : 4441 total number of charged atoms : 4271 net assigned charge : 4.500036 assigned positive charge : 680.2418 centred at (gu) : 91.88156 89.72353 87.59791 assigned negative charge : -675.7448 centred at (gu) : 91.87117 89.65858 87.63157 start vw surface at 0.2000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8544 nv = 96 ne = 84 npr = 89077 no. pairs analyzed = 89077 no. exposed pairs = 5593 no. arc points = 38213 no. surface atoms = 1863 nbur = 2578 mkacc time = 0.3000000 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= 335 mr = 4517 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 4340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3980 ## 546 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 11401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1149506E-09 -3.4521056E-11 midg,1,midg; midg,igrid,midg -4.2079087E-10 8.6383994E-10 1,midg,midg; igrid,midg,midg 1.0822425E-10 5.9891109E-10 gauss-seidel spectral radius is 0.9828377 estimated iterations to convergence 63 setup time was (sec) 0.8800000 now iterating at: 16:47:06 rms-change max change #iterations 9.1477610E-02 14.39726 at 10iterations 6.4523309E-03 0.9189491 at 20iterations 9.3724002E-04 0.1320992 at 30iterations 3.0370516E-04 4.0670395E-02 at 40iterations 1.1478777E-04 1.4688015E-02 at 50iterations finished qdiffx linear iterations at : 16:47:10 total time elapsed so far: 4.440000 # loops : 50 mean,max change (kT/e) : 1.1478777E-04 1.4688015E-02 energy calculations done at 4.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 16:47:10 4.663u 0.446s 0:05.40 94.4% 0+0k 0+0io 5pf+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 16:47:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4441 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: 1.639168 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): 15.68100 78.81600 ymin,ymax (A): 120.1650 185.3200 zmin,zma (A): -1.378000 60.16200 x,y,z range (A): 63.13500 65.15499 61.54000 scale (grids/A): 1.639168 object centre (A): 47.24850 152.7425 29.39200 number of atom coordinates read : 4441 total number of charged atoms : 4271 net assigned charge : 4.500036 assigned positive charge : 680.2418 centred at (gu) : 95.64351 89.16946 82.79295 assigned negative charge : -675.7448 centred at (gu) : 95.61304 88.97548 82.89453 start vw surface at 0.2100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 95642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38213 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30144 mr = 66523 m= 3358 mr = 20382 m= 106 mr = 1713 m= 0 mr = 11 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 554 time to turn everything in is 0.9700000 number of dielectric boundary points 40621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 444 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 32655 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) : 0.5463895 object centre at (A) : 47.24850 152.7425 29.39200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9529743E-03 8.0777770E-03 midg,1,midg; midg,igrid,midg 1.1905296E-02 3.0643320E-02 1,midg,midg; igrid,midg,midg -1.0733158E-02 -1.3134819E-02 gauss-seidel spectral radius is 0.9983449 estimated iterations to convergence 195 setup time was (sec) 1.310000 now iterating at: 16:47:12 rms-change max change #iterations 4.241021 164.8254 at 10iterations 1.830188 62.06188 at 20iterations 0.7938261 24.68277 at 30iterations 0.3444937 10.43937 at 40iterations 0.1497381 4.503040 at 50iterations 6.5011710E-02 2.078759 at 60iterations 2.8407391E-02 0.9476280 at 70iterations 1.2428289E-02 0.4061203 at 80iterations 5.5058054E-03 0.1659622 at 90iterations 2.5061083E-03 8.2632065E-02 at 100iterations 1.1972686E-03 3.8589478E-02 at 110iterations 6.2148744E-04 1.9474983E-02 at 120iterations finished qdiffx linear iterations at : 16:47:21 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 6.2148744E-04 1.9474983E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.74000 DelPhi exited at 16:47:22 10.748u 0.487s 0:11.54 97.2% 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 Sat Oct 8 2011 at 16:47:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4441 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: 2.458753 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): 15.68100 78.81600 ymin,ymax (A): 120.1650 185.3200 zmin,zma (A): -1.378000 60.16200 x,y,z range (A): 63.13500 65.15499 61.54000 scale (grids/A): 2.458753 object centre (A): 47.24850 152.7425 29.39200 number of atom coordinates read : 4441 total number of charged atoms : 4271 net assigned charge : 4.500036 assigned positive charge : 680.2418 centred at (gu) : 98.46475 88.75402 79.18919 assigned negative charge : -675.7448 centred at (gu) : 98.41968 88.46306 79.34174 start vw surface at 0.2200000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 222498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38213 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 104411 mr = 162879 m= 30011 mr = 82110 m= 5320 mr = 22185 m= 455 mr = 3640 m= 10 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 1.490000 no. cavity mid-points inaccessible to solvent = 1774 time to turn everything in is 2.440000 number of dielectric boundary points 91674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.600000 number of grid points assigned charge 34136 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) : 1.639168 object centre at (A) : 47.24850 152.7425 29.39200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6312656E-02 0.1797880 midg,1,midg; midg,igrid,midg 0.1972661 0.4740884 1,midg,midg; igrid,midg,midg -0.1577862 -0.2277543 gauss-seidel spectral radius is 0.9992200 estimated iterations to convergence 283 setup time was (sec) 2.800000 now iterating at: 16:47:25 rms-change max change #iterations 11.01345 311.5495 at 10iterations 6.432099 139.0046 at 20iterations 3.727427 71.77258 at 30iterations 2.151117 41.35017 at 40iterations 1.237586 23.00406 at 50iterations 0.7088632 14.78097 at 60iterations 0.4048038 7.980166 at 70iterations 0.2307474 4.474202 at 80iterations 0.1316278 2.393612 at 90iterations 7.4729025E-02 1.277444 at 100iterations 4.2592224E-02 0.7386799 at 110iterations 2.4218509E-02 0.4377441 at 120iterations 1.3771098E-02 0.2623711 at 130iterations 7.8421999E-03 0.1352139 at 140iterations 4.4736085E-03 7.9262018E-02 at 150iterations 2.5659450E-03 4.2667389E-02 at 160iterations 1.4883436E-03 2.6439667E-02 at 170iterations 8.7628257E-04 1.5552521E-02 at 180iterations finished qdiffx linear iterations at : 16:47:41 total time elapsed so far: 18.54000 # loops : 180 mean,max change (kT/e) : 8.7628257E-04 1.5552521E-02 energy calculations done at 18.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.99000 DelPhi exited at 16:47:42 18.990u 0.512s 0:19.78 98.5% 0+0k 0+0io 0pf+0w