Mon Oct 10 17:04:04 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 Mon Oct 10 2011 at 17:04:04 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIT 1162 has a net charge of 0.5140 !!! WARNING: HIR 1202 has a net charge of 0.5140 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: 0.5954871 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 0.5954871 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.028025 assigned positive charge : 400.7965 centred at (gu) : 90.07649 88.97230 90.16518 assigned negative charge : -391.7693 centred at (gu) : 90.02047 88.94648 90.27013 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6397 nv = 96 ne = 84 npr = 53842 no. pairs analyzed = 53842 no. exposed pairs = 3455 no. arc points = 24461 no. surface atoms = 1159 nbur = 1539 mkacc time = 0.1400000 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 = 1.456000 m= 283 mr = 3330 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2482 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4194476E-09 -5.5696336E-11 midg,1,midg; midg,igrid,midg 3.1568530E-09 3.3212080E-09 1,midg,midg; igrid,midg,midg 1.5223636E-09 5.2184741E-09 gauss-seidel spectral radius is 0.9854217 estimated iterations to convergence 68 setup time was (sec) 0.6200000 now iterating at: 17:04:05 rms-change max change #iterations 0.1106882 18.27919 at 10iterations 9.1969594E-03 1.507254 at 20iterations 7.4697653E-04 0.1023674 at 30iterations 6.3655105E-05 8.6450577E-03 at 40iterations 5.6606395E-06 1.0185242E-03 at 50iterations finished qdiffx linear iterations at : 17:04:09 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 5.6606395E-06 1.0185242E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 17:04:10 4.455u 0.387s 0:05.69 84.8% 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 Mon Oct 10 2011 at 17:04:10 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIT 1162 has a net charge of 0.5140 !!! WARNING: HIR 1202 has a net charge of 0.5140 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: 1.786461 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 1.786461 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.028025 assigned positive charge : 400.7965 centred at (gu) : 90.22894 86.91597 90.49464 assigned negative charge : -391.7693 centred at (gu) : 90.06116 86.83900 90.81017 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70030 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24461 grid for indexing accessible points = 1.400000 m= 22656 mr = 47368 m= 2899 mr = 15867 m= 126 mr = 1485 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1286 time to turn everything in is 0.5700000 number of dielectric boundary points 30959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19986 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) : 0.5954871 object centre at (A) : 3.903500 3.053500 22.40400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0518644E-02 1.3521868E-02 midg,1,midg; midg,igrid,midg 1.7072821E-02 9.1245637E-04 1,midg,midg; igrid,midg,midg 4.0595061E-03 7.5082793E-03 gauss-seidel spectral radius is 0.9984655 estimated iterations to convergence 202 setup time was (sec) 0.8700000 now iterating at: 17:04:11 rms-change max change #iterations 3.752710 177.4931 at 10iterations 1.668700 63.78436 at 20iterations 0.7459506 26.15029 at 30iterations 0.3338922 11.45161 at 40iterations 0.1488114 5.087540 at 50iterations 6.6567443E-02 2.328653 at 60iterations 2.9641533E-02 0.9595428 at 70iterations 1.3261636E-02 0.4662390 at 80iterations 5.9376378E-03 0.2008610 at 90iterations 2.6592221E-03 8.7943077E-02 at 100iterations 1.1902323E-03 4.0375233E-02 at 110iterations 5.3228624E-04 1.7050266E-02 at 120iterations finished qdiffx linear iterations at : 17:04:21 total time elapsed so far: 11.16000 # loops : 120 mean,max change (kT/e) : 5.3228624E-04 1.7050266E-02 energy calculations done at 11.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 17:04:22 11.332u 0.459s 0:12.55 93.8% 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 Mon Oct 10 2011 at 17:04:23 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIT 1162 has a net charge of 0.5140 !!! WARNING: HIR 1202 has a net charge of 0.5140 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: 2.679692 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 2.679692 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.028025 assigned positive charge : 400.7965 centred at (gu) : 90.34338 85.37392 90.74178 assigned negative charge : -391.7693 centred at (gu) : 90.09160 85.25838 91.21521 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 162453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24461 grid for indexing accessible points = 1.400000 m= 75769 mr = 115540 m= 24148 mr = 60380 m= 4844 mr = 18372 m= 529 mr = 3260 m= 27 mr = 286 m= 0 mr = 8 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 4307 time to turn everything in is 1.420000 number of dielectric boundary points 69924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 20485 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) : 1.786461 object centre at (A) : 3.903500 3.053500 22.40400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6097769 0.1724961 midg,1,midg; midg,igrid,midg 0.3163378 4.8398126E-02 1,midg,midg; igrid,midg,midg 5.8051303E-02 5.9942104E-02 gauss-seidel spectral radius is 0.9992165 estimated iterations to convergence 282 setup time was (sec) 1.740000 now iterating at: 17:04:25 rms-change max change #iterations 9.156762 410.0371 at 10iterations 5.266703 113.8554 at 20iterations 3.010370 78.19919 at 30iterations 1.716548 37.65222 at 40iterations 0.9725819 23.63205 at 50iterations 0.5524676 12.35373 at 60iterations 0.3133599 6.295937 at 70iterations 0.1771187 3.688133 at 80iterations 0.1000185 2.184173 at 90iterations 5.6588188E-02 1.264339 at 100iterations 3.2078430E-02 0.7047164 at 110iterations 1.8157307E-02 0.3486875 at 120iterations 1.0217507E-02 0.1919796 at 130iterations 5.7740919E-03 0.1125336 at 140iterations 3.2770883E-03 7.1041107E-02 at 150iterations 1.8489952E-03 3.4602880E-02 at 160iterations 1.0481159E-03 2.0763397E-02 at 170iterations 5.9414568E-04 1.1337280E-02 at 180iterations finished qdiffx linear iterations at : 17:04:40 total time elapsed so far: 17.27000 # loops : 180 mean,max change (kT/e) : 5.9414568E-04 1.1337280E-02 energy calculations done at 17.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.43000 DelPhi exited at 17:04:41 17.438u 0.494s 0:18.29 97.9% 0+0k 0+0io 0pf+0w