Tue Oct 11 04:54:11 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 Tue Oct 11 2011 at 04:54:11 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 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: 0.6324391 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): -72.13700 -15.84700 ymin,ymax (A): -49.54800 2.728000 zmin,zma (A): 4.330000 60.58600 x,y,z range (A): 56.29000 52.27600 56.25600 scale (grids/A): 0.6324391 object centre (A): -43.99200 -23.41000 32.45800 number of atom coordinates read : 2857 total number of charged atoms : 2710 net assigned charge : 8.000018 assigned positive charge : 438.4706 centred at (gu) : 90.44247 90.01966 91.01893 assigned negative charge : -430.4713 centred at (gu) : 90.40821 89.74345 90.92392 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7693 nv = 96 ne = 84 npr = 56188 no. pairs analyzed = 56188 no. exposed pairs = 3645 no. arc points = 25547 no. surface atoms = 1229 nbur = 1628 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 431 mr = 4149 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3400000 number of dielectric boundary points 3940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2636 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7042254E-10 2.3835483E-08 midg,1,midg; midg,igrid,midg -2.0555007E-08 3.7544496E-08 1,midg,midg; igrid,midg,midg 5.1636975E-09 1.4101653E-08 gauss-seidel spectral radius is 0.9870753 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 04:54:12 rms-change max change #iterations 0.1449382 23.20467 at 10iterations 1.4385778E-02 2.001942 at 20iterations 1.3898138E-03 0.1757880 at 30iterations 1.3929831E-04 2.1190166E-02 at 40iterations 1.6133243E-05 2.8476715E-03 at 50iterations finished qdiffx linear iterations at : 04:54:15 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 1.6133243E-05 2.8476715E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 04:54:16 3.730u 0.232s 0:04.27 92.7% 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 Tue Oct 11 2011 at 04:54:16 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 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: 1.897317 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): -72.13700 -15.84700 ymin,ymax (A): -49.54800 2.728000 zmin,zma (A): 4.330000 60.58600 x,y,z range (A): 56.29000 52.27600 56.25600 scale (grids/A): 1.897317 object centre (A): -43.99200 -23.41000 32.45800 number of atom coordinates read : 2857 total number of charged atoms : 2710 net assigned charge : 8.000018 assigned positive charge : 438.4706 centred at (gu) : 91.32654 90.05846 93.05613 assigned negative charge : -430.4713 centred at (gu) : 91.22415 89.23021 92.77139 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 82034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25547 grid for indexing accessible points = 1.400000 m= 30443 mr = 55957 m= 5052 mr = 22277 m= 290 mr = 3167 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 654 time to turn everything in is 0.6400000 number of dielectric boundary points 36335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21284 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) : 0.6324391 object centre at (A) : -43.99200 -23.41000 32.45800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5693907E-02 4.5579590E-02 midg,1,midg; midg,igrid,midg -3.1852387E-02 5.4321382E-02 1,midg,midg; igrid,midg,midg 1.4193847E-03 3.0418634E-04 gauss-seidel spectral radius is 0.9986610 estimated iterations to convergence 217 setup time was (sec) 0.9600000 now iterating at: 04:54:17 rms-change max change #iterations 4.522212 182.4853 at 10iterations 2.122784 71.88371 at 20iterations 1.002689 34.60993 at 30iterations 0.4725405 14.52896 at 40iterations 0.2231092 6.615357 at 50iterations 0.1053994 3.294691 at 60iterations 4.9466062E-02 1.482841 at 70iterations 2.3408161E-02 0.7363979 at 80iterations 1.1041677E-02 0.3265872 at 90iterations 5.2069640E-03 0.1644478 at 100iterations 2.4622995E-03 7.6086044E-02 at 110iterations 1.1612101E-03 3.9413452E-02 at 120iterations finished qdiffx linear iterations at : 04:54:24 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 1.1612101E-03 3.9413452E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 04:54:25 8.579u 0.282s 0:09.28 95.3% 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 Tue Oct 11 2011 at 04:54:25 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 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: 2.845976 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): -72.13700 -15.84700 ymin,ymax (A): -49.54800 2.728000 zmin,zma (A): 4.330000 60.58600 x,y,z range (A): 56.29000 52.27600 56.25600 scale (grids/A): 2.845976 object centre (A): -43.99200 -23.41000 32.45800 number of atom coordinates read : 2857 total number of charged atoms : 2710 net assigned charge : 8.000018 assigned positive charge : 438.4706 centred at (gu) : 91.98990 90.08752 94.58426 assigned negative charge : -430.4713 centred at (gu) : 91.83614 88.84520 94.15689 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 189361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25547 grid for indexing accessible points = 1.400000 m= 96815 mr = 135707 m= 36771 mr = 78710 m= 9139 mr = 29559 m= 1187 mr = 6746 m= 49 mr = 738 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2343 time to turn everything in is 1.660000 number of dielectric boundary points 81850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 21676 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) : 1.897317 object centre at (A) : -43.99200 -23.41000 32.45800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4934518E-02 0.3040963 midg,1,midg; midg,igrid,midg -0.3387743 0.4073110 1,midg,midg; igrid,midg,midg -0.1406555 7.2578423E-02 gauss-seidel spectral radius is 0.9992706 estimated iterations to convergence 292 setup time was (sec) 2.010000 now iterating at: 04:54:27 rms-change max change #iterations 10.51236 415.0006 at 10iterations 6.154992 174.2797 at 20iterations 3.594857 71.96458 at 30iterations 2.090424 42.38437 at 40iterations 1.216351 23.97508 at 50iterations 0.7057923 13.78957 at 60iterations 0.4091939 9.043612 at 70iterations 0.2365993 4.746758 at 80iterations 0.1367060 2.524133 at 90iterations 7.8975424E-02 1.385128 at 100iterations 4.5584388E-02 0.8097725 at 110iterations 2.6361167E-02 0.4455171 at 120iterations 1.5214513E-02 0.2697556 at 130iterations 8.7861745E-03 0.1488075 at 140iterations 5.0770375E-03 8.5159302E-02 at 150iterations 2.9354687E-03 4.8568726E-02 at 160iterations 1.6902675E-03 3.0838013E-02 at 170iterations 9.7968942E-04 1.6429901E-02 at 180iterations finished qdiffx linear iterations at : 04:54:39 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 9.7968942E-04 1.6429901E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 04:54:39 13.505u 0.273s 0:14.34 96.0% 0+0k 0+0io 0pf+0w