Sun Oct 9 07:28:49 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 Sun Oct 9 2011 at 07:28:49 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2655 !!! WARNING: NAP 319 has a net charge of -3.1550 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: 0.5546381 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): -18.52100 27.09100 ymin,ymax (A): 18.19100 82.37700 zmin,zma (A): -8.924000 47.12800 x,y,z range (A): 45.61200 64.18600 56.05200 scale (grids/A): 0.5546381 object centre (A): 4.285000 50.28400 19.10200 number of atom coordinates read : 2655 total number of charged atoms : 2460 net assigned charge : -15.65498 assigned positive charge : 391.8098 centred at (gu) : 90.40335 89.46483 88.97135 assigned negative charge : -407.4652 centred at (gu) : 90.13451 89.53374 88.80604 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5337 nv = 96 ne = 84 npr = 54420 no. pairs analyzed = 54420 no. exposed pairs = 3437 no. arc points = 24941 no. surface atoms = 1171 nbur = 1484 mkacc time = 0.1200000 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= 198 mr = 2679 m= 0 mr = 9 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.2800000 number of dielectric boundary points 2847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2445 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5534391E-09 -1.0081361E-11 midg,1,midg; midg,igrid,midg -8.8205482E-10 -1.7012604E-09 1,midg,midg; igrid,midg,midg -3.3341661E-09 9.1761826E-10 gauss-seidel spectral radius is 0.9832131 estimated iterations to convergence 64 setup time was (sec) 0.5400000 now iterating at: 07:28:49 rms-change max change #iterations 7.5217433E-02 15.14381 at 10iterations 5.0213910E-03 1.163205 at 20iterations 3.4452579E-04 5.1858902E-02 at 30iterations 2.4840294E-05 3.9479733E-03 at 40iterations 1.9873098E-06 3.0708313E-04 at 50iterations finished qdiffx linear iterations at : 07:28:52 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.9873098E-06 3.0708313E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 07:28:53 3.419u 0.191s 0:03.87 93.0% 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 Sun Oct 9 2011 at 07:28:53 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2655 !!! WARNING: NAP 319 has a net charge of -3.1550 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: 1.663914 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): -18.52100 27.09100 ymin,ymax (A): 18.19100 82.37700 zmin,zma (A): -8.924000 47.12800 x,y,z range (A): 45.61200 64.18600 56.05200 scale (grids/A): 1.663914 object centre (A): 4.285000 50.28400 19.10200 number of atom coordinates read : 2655 total number of charged atoms : 2460 net assigned charge : -15.65498 assigned positive charge : 391.8098 centred at (gu) : 91.20953 88.39397 86.91354 assigned negative charge : -407.4652 centred at (gu) : 90.40320 88.60078 86.41790 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 58257 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24941 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17697 mr = 38039 m= 1667 mr = 12300 m= 30 mr = 793 m= 0 mr = 5 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 758 time to turn everything in is 0.4500000 number of dielectric boundary points 26514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 18928 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) : 0.5546381 object centre at (A) : 4.285000 50.28400 19.10200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3183111E-02 -2.2251923E-03 midg,1,midg; midg,igrid,midg -2.6996225E-02 -4.9943056E-02 1,midg,midg; igrid,midg,midg -2.3108430E-02 3.8756724E-03 gauss-seidel spectral radius is 0.9982132 estimated iterations to convergence 188 setup time was (sec) 0.7500000 now iterating at: 07:28:54 rms-change max change #iterations 3.257452 197.8275 at 10iterations 1.371637 67.68503 at 20iterations 0.5757558 23.93247 at 30iterations 0.2414910 9.372766 at 40iterations 0.1014846 4.079915 at 50iterations 4.2233981E-02 1.541056 at 60iterations 1.7728057E-02 0.6957455 at 70iterations 7.4489200E-03 0.2828140 at 80iterations 3.1278254E-03 0.1203537 at 90iterations 1.3121872E-03 4.6417236E-02 at 100iterations 5.5089925E-04 2.0195007E-02 at 110iterations 2.3100745E-04 8.7630749E-03 at 120iterations finished qdiffx linear iterations at : 07:29:00 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 2.3100745E-04 8.7630749E-03 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 07:29:01 7.613u 0.228s 0:08.12 96.4% 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 Sun Oct 9 2011 at 07:29:01 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2655 !!! WARNING: NAP 319 has a net charge of -3.1550 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: 2.495872 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): -18.52100 27.09100 ymin,ymax (A): 18.19100 82.37700 zmin,zma (A): -8.924000 47.12800 x,y,z range (A): 45.61200 64.18600 56.05200 scale (grids/A): 2.495872 object centre (A): 4.285000 50.28400 19.10200 number of atom coordinates read : 2655 total number of charged atoms : 2460 net assigned charge : -15.65498 assigned positive charge : 391.8098 centred at (gu) : 91.81417 87.59080 85.37009 assigned negative charge : -407.4652 centred at (gu) : 90.60473 87.90099 84.62675 start vw surface at 0.1500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 134919 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24941 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61349 mr = 92962 m= 17039 mr = 48555 m= 2435 mr = 12982 m= 145 mr = 1542 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2509 time to turn everything in is 1.020000 number of dielectric boundary points 59779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 19662 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) : 1.663914 object centre at (A) : 4.285000 50.28400 19.10200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2854453 -2.5825843E-02 midg,1,midg; midg,igrid,midg -0.4088027 -0.6987818 1,midg,midg; igrid,midg,midg -0.3287132 7.1830429E-02 gauss-seidel spectral radius is 0.9991385 estimated iterations to convergence 269 setup time was (sec) 1.340000 now iterating at: 07:29:02 rms-change max change #iterations 8.414524 366.8980 at 10iterations 4.715894 117.3534 at 20iterations 2.647597 75.95707 at 30iterations 1.477632 37.80270 at 40iterations 0.8216515 21.18192 at 50iterations 0.4577132 11.28233 at 60iterations 0.2535968 6.247759 at 70iterations 0.1401200 3.464349 at 80iterations 7.7334628E-02 1.875413 at 90iterations 4.2727597E-02 1.042613 at 100iterations 2.3597876E-02 0.5976820 at 110iterations 1.2991361E-02 0.2957357 at 120iterations 7.1565481E-03 0.1697087 at 130iterations 3.9354586E-03 8.9635849E-02 at 140iterations 2.1699755E-03 5.6326866E-02 at 150iterations 1.1926712E-03 2.7362823E-02 at 160iterations 6.5667700E-04 1.4760017E-02 at 170iterations 3.6143721E-04 8.1615448E-03 at 180iterations finished qdiffx linear iterations at : 07:29:13 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 3.6143721E-04 8.1615448E-03 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 07:29:14 12.276u 0.301s 0:12.85 97.8% 0+0k 0+0io 0pf+0w