Sun Oct 9 08:56:48 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 Sun Oct 9 2011 at 08:56:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6063 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.4826006 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): 15.03200 84.70800 ymin,ymax (A): 15.35900 84.92400 zmin,zma (A): -5.153000 68.61400 x,y,z range (A): 69.67600 69.56500 73.76700 scale (grids/A): 0.4826006 object centre (A): 49.87000 50.14150 31.73050 number of atom coordinates read : 6063 total number of charged atoms : 5893 net assigned charge : -3.499983 assigned positive charge : 915.1446 centred at (gu) : 90.11052 89.79807 91.33916 assigned negative charge : -918.6530 centred at (gu) : 90.11889 89.82312 91.42859 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8950 nv = 96 ne = 84 npr = 120400 no. pairs analyzed = 120400 no. exposed pairs = 7673 no. arc points = 53023 no. surface atoms = 2571 nbur = 3492 mkacc time = 0.2600000 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 = 1.764000 m= 306 mr = 4593 m= 0 mr = 5 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5073 ## 863 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 12104 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8619352E-11 -1.4167537E-10 midg,1,midg; midg,igrid,midg 1.2131942E-11 -3.3671427E-11 1,midg,midg; igrid,midg,midg -4.0507779E-12 -2.0485566E-11 gauss-seidel spectral radius is 0.9781478 estimated iterations to convergence 56 setup time was (sec) 0.7700000 now iterating at: 08:56:49 rms-change max change #iterations 5.4649875E-02 7.756325 at 10iterations 2.9968009E-03 0.4512367 at 20iterations 4.6819737E-04 0.1034908 at 30iterations 1.5143873E-04 3.3088684E-02 at 40iterations 5.2647210E-05 1.1009216E-02 at 50iterations finished qdiffx linear iterations at : 08:56:52 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 5.2647210E-05 1.1009216E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 08:56:52 3.582u 0.211s 0:04.16 91.1% 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 08:56:52 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 = 6063 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: 1.447802 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): 15.03200 84.70800 ymin,ymax (A): 15.35900 84.92400 zmin,zma (A): -5.153000 68.61400 x,y,z range (A): 69.67600 69.56500 73.76700 scale (grids/A): 1.447802 object centre (A): 49.87000 50.14150 31.73050 number of atom coordinates read : 6063 total number of charged atoms : 5893 net assigned charge : -3.499983 assigned positive charge : 915.1446 centred at (gu) : 90.32977 89.39230 94.01576 assigned negative charge : -918.6530 centred at (gu) : 90.35644 89.46910 94.28568 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 102332 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53023 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 28452 mr = 70300 m= 1947 mr = 18286 m= 35 mr = 642 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 360 time to turn everything in is 0.7000000 number of dielectric boundary points 43538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 889 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 43312 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) : 0.4826006 object centre at (A) : 49.87000 50.14150 31.73050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9527054E-03 -3.1479049E-02 midg,1,midg; midg,igrid,midg -3.8730931E-03 -1.3627726E-02 1,midg,midg; igrid,midg,midg 4.5206486E-03 -3.1768645E-03 gauss-seidel spectral radius is 0.9979848 estimated iterations to convergence 177 setup time was (sec) 1.000000 now iterating at: 08:56:53 rms-change max change #iterations 3.833009 164.4344 at 10iterations 1.524047 54.95325 at 20iterations 0.6066375 18.03188 at 30iterations 0.2419437 8.150788 at 40iterations 9.6801102E-02 2.846407 at 50iterations 3.8754061E-02 1.127792 at 60iterations 1.5498443E-02 0.4980297 at 70iterations 6.2675122E-03 0.1894503 at 80iterations 2.5891147E-03 8.0339313E-02 at 90iterations 1.1152202E-03 4.6449661E-02 at 100iterations 5.2363693E-04 2.0643234E-02 at 110iterations 2.7829420E-04 1.1027336E-02 at 120iterations finished qdiffx linear iterations at : 08:57:00 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.7829420E-04 1.1027336E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 08:57:01 7.819u 0.219s 0:08.39 95.5% 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 08:57:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6063 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.171703 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): 15.03200 84.70800 ymin,ymax (A): 15.35900 84.92400 zmin,zma (A): -5.153000 68.61400 x,y,z range (A): 69.67600 69.56500 73.76700 scale (grids/A): 2.171703 object centre (A): 49.87000 50.14150 31.73050 number of atom coordinates read : 6063 total number of charged atoms : 5893 net assigned charge : -3.499983 assigned positive charge : 915.1446 centred at (gu) : 90.49397 89.08792 96.02306 assigned negative charge : -918.6530 centred at (gu) : 90.53447 89.20340 96.42840 start vw surface at 0.2400000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 238865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53023 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 104502 mr = 173218 m= 23503 mr = 80521 m= 2518 mr = 16218 m= 78 mr = 1340 m= 0 mr = 2 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1067 time to turn everything in is 1.740000 number of dielectric boundary points 98167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 46873 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) : 1.447802 object centre at (A) : 49.87000 50.14150 31.73050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2204833 -0.9885827 midg,1,midg; midg,igrid,midg -0.1411537 -0.2887252 1,midg,midg; igrid,midg,midg 0.1261614 -7.6037593E-02 gauss-seidel spectral radius is 0.9991606 estimated iterations to convergence 273 setup time was (sec) 2.050000 now iterating at: 08:57:03 rms-change max change #iterations 10.85402 278.5130 at 10iterations 6.238283 130.1443 at 20iterations 3.576079 75.70094 at 30iterations 2.034396 42.51461 at 40iterations 1.155550 29.25504 at 50iterations 0.6513698 13.27217 at 60iterations 0.3671412 7.690816 at 70iterations 0.2063012 4.072172 at 80iterations 0.1155017 2.205508 at 90iterations 6.4763755E-02 1.215672 at 100iterations 3.6179651E-02 0.6904585 at 110iterations 2.0204313E-02 0.3732605 at 120iterations 1.1292171E-02 0.1988010 at 130iterations 6.3148998E-03 0.1130829 at 140iterations 3.5306443E-03 6.3936234E-02 at 150iterations 1.9763364E-03 3.5129547E-02 at 160iterations 1.1124408E-03 2.1312714E-02 at 170iterations 6.2895293E-04 1.1625290E-02 at 180iterations finished qdiffx linear iterations at : 08:57:14 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 6.2895293E-04 1.1625290E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 08:57:15 13.656u 0.227s 0:14.19 97.7% 0+0k 0+0io 0pf+0w