Sun Oct 9 00:15:45 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 00:15:45 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5679733 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): -40.66200 16.50700 ymin,ymax (A): -53.08200 9.597000 zmin,zma (A): -13.34100 48.76600 x,y,z range (A): 57.16900 62.67900 62.10700 scale (grids/A): 0.5679733 object centre (A): -12.07750 -21.74250 17.71250 number of atom coordinates read : 3381 total number of charged atoms : 3239 net assigned charge : 15.24003 assigned positive charge : 501.1436 centred at (gu) : 90.27052 90.38094 89.15087 assigned negative charge : -485.9052 centred at (gu) : 90.40358 90.52809 89.02247 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7559 nv = 96 ne = 84 npr = 64907 no. pairs analyzed = 64907 no. exposed pairs = 4492 no. arc points = 32938 no. surface atoms = 1499 nbur = 1882 mkacc time = 0.1500000 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 = 1.512000 m= 327 mr = 3783 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3600000 number of dielectric boundary points 4083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3407 ## 403 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2717366E-10 3.4674954E-09 midg,1,midg; midg,igrid,midg 4.1357087E-09 -2.1368345E-10 1,midg,midg; igrid,midg,midg 4.0408019E-09 4.4409556E-11 gauss-seidel spectral radius is 0.9840564 estimated iterations to convergence 65 setup time was (sec) 0.5700000 now iterating at: 00:15:45 rms-change max change #iterations 9.6076347E-02 14.87485 at 10iterations 7.1708444E-03 1.082237 at 20iterations 5.4668752E-04 8.8321686E-02 at 30iterations 5.1318337E-05 8.1262589E-03 at 40iterations 7.1166924E-06 6.9427490E-04 at 50iterations finished qdiffx linear iterations at : 00:15:48 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 7.1166924E-06 6.9427490E-04 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 00:15:48 3.217u 0.162s 0:03.71 90.8% 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 00:15:48 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.703920 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): -40.66200 16.50700 ymin,ymax (A): -53.08200 9.597000 zmin,zma (A): -13.34100 48.76600 x,y,z range (A): 57.16900 62.67900 62.10700 scale (grids/A): 1.703920 object centre (A): -12.07750 -21.74250 17.71250 number of atom coordinates read : 3381 total number of charged atoms : 3239 net assigned charge : 15.24003 assigned positive charge : 501.1436 centred at (gu) : 90.81061 91.14193 87.45187 assigned negative charge : -485.9052 centred at (gu) : 91.21040 91.58417 87.06685 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 82825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32938 grid for indexing accessible points = 1.400000 m= 27514 mr = 55112 m= 3334 mr = 19300 m= 101 mr = 1706 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1283 time to turn everything in is 0.5800000 number of dielectric boundary points 37646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 25027 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) : 0.5679733 object centre at (A) : -12.07750 -21.74250 17.71250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2217531E-02 4.7461387E-02 midg,1,midg; midg,igrid,midg 3.5904415E-02 6.1263037E-03 1,midg,midg; igrid,midg,midg 1.7643191E-02 -3.3877490E-03 gauss-seidel spectral radius is 0.9984005 estimated iterations to convergence 198 setup time was (sec) 0.8500000 now iterating at: 00:15:49 rms-change max change #iterations 3.888262 157.1261 at 10iterations 1.696924 69.48945 at 20iterations 0.7455841 25.63750 at 30iterations 0.3274066 10.16360 at 40iterations 0.1439670 4.931446 at 50iterations 6.3165836E-02 1.933075 at 60iterations 2.7728986E-02 0.9276280 at 70iterations 1.2169458E-02 0.3757493 at 80iterations 5.3553768E-03 0.1723105 at 90iterations 2.3537907E-03 7.9223633E-02 at 100iterations 1.0379034E-03 3.6374569E-02 at 110iterations 4.5700188E-04 1.6058922E-02 at 120iterations finished qdiffx linear iterations at : 00:15:56 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 4.5700188E-04 1.6058922E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 00:15:56 7.180u 0.220s 0:07.73 95.7% 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 00:15:56 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.555880 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): -40.66200 16.50700 ymin,ymax (A): -53.08200 9.597000 zmin,zma (A): -13.34100 48.76600 x,y,z range (A): 57.16900 62.67900 62.10700 scale (grids/A): 2.555880 object centre (A): -12.07750 -21.74250 17.71250 number of atom coordinates read : 3381 total number of charged atoms : 3239 net assigned charge : 15.24003 assigned positive charge : 501.1436 centred at (gu) : 91.21582 91.71270 86.17768 assigned negative charge : -485.9052 centred at (gu) : 91.81561 92.37608 85.60023 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 192000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32938 grid for indexing accessible points = 1.400000 m= 92393 mr = 135126 m= 29156 mr = 73153 m= 5303 mr = 22324 m= 460 mr = 3598 m= 4 mr = 214 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 4398 time to turn everything in is 1.390000 number of dielectric boundary points 84901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 25887 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) : 1.703920 object centre at (A) : -12.07750 -21.74250 17.71250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1395666 0.7052772 midg,1,midg; midg,igrid,midg 0.5317379 0.2223054 1,midg,midg; igrid,midg,midg 0.2438410 -3.8474921E-02 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 1.680000 now iterating at: 00:15:58 rms-change max change #iterations 9.823185 346.7678 at 10iterations 5.696609 126.9228 at 20iterations 3.276611 78.50240 at 30iterations 1.877257 41.92509 at 40iterations 1.073906 25.91795 at 50iterations 0.6132935 12.73805 at 60iterations 0.3484813 6.813119 at 70iterations 0.1975186 3.922495 at 80iterations 0.1119837 2.783272 at 90iterations 6.3644581E-02 1.254528 at 100iterations 3.5982598E-02 0.6766586 at 110iterations 2.0380108E-02 0.3886528 at 120iterations 1.1539313E-02 0.2230625 at 130iterations 6.5272739E-03 0.1231651 at 140iterations 3.6958179E-03 7.2817802E-02 at 150iterations 2.0864035E-03 4.3183804E-02 at 160iterations 1.1820209E-03 2.2867203E-02 at 170iterations 6.6711457E-04 1.2365341E-02 at 180iterations finished qdiffx linear iterations at : 00:16:08 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 6.6711457E-04 1.2365341E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 00:16:08 11.634u 0.224s 0:12.15 97.5% 0+0k 0+0io 0pf+0w