Tue Oct 11 04:29:54 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 Tue Oct 11 2011 at 04:29:54 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 = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6373760 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): -11.66700 36.58200 ymin,ymax (A): -25.74800 22.54300 zmin,zma (A): -10.40100 45.45300 x,y,z range (A): 48.24900 48.29100 55.85400 scale (grids/A): 0.6373760 object centre (A): 12.45750 -1.602500 17.52600 number of atom coordinates read : 2744 total number of charged atoms : 2596 net assigned charge : 3.500012 assigned positive charge : 416.1166 centred at (gu) : 90.15550 90.39886 92.01271 assigned negative charge : -412.6172 centred at (gu) : 89.90547 90.22988 91.96803 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7262 nv = 96 ne = 84 npr = 56701 no. pairs analyzed = 56701 no. exposed pairs = 3336 no. arc points = 23168 no. surface atoms = 1120 nbur = 1624 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 4048 m= 0 mr = 35 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2350 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8927 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5029568E-10 1.4859511E-08 midg,1,midg; midg,igrid,midg -1.3982730E-08 2.5711715E-08 1,midg,midg; igrid,midg,midg -2.4188628E-08 3.3596006E-08 gauss-seidel spectral radius is 0.9872553 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 04:29:55 rms-change max change #iterations 0.1478113 20.80681 at 10iterations 1.4806842E-02 2.272217 at 20iterations 1.5207666E-03 0.2196445 at 30iterations 1.5994553E-04 2.6079178E-02 at 40iterations 2.0351068E-05 3.0727386E-03 at 50iterations finished qdiffx linear iterations at : 04:29:58 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 2.0351068E-05 3.0727386E-03 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 04:29:58 3.802u 0.175s 0:04.28 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 04:29:58 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 = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.912128 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): -11.66700 36.58200 ymin,ymax (A): -25.74800 22.54300 zmin,zma (A): -10.40100 45.45300 x,y,z range (A): 48.24900 48.29100 55.85400 scale (grids/A): 1.912128 object centre (A): 12.45750 -1.602500 17.52600 number of atom coordinates read : 2744 total number of charged atoms : 2596 net assigned charge : 3.500012 assigned positive charge : 416.1166 centred at (gu) : 90.46577 91.19587 96.03747 assigned negative charge : -412.6172 centred at (gu) : 89.71608 90.68924 95.90364 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23168 grid for indexing accessible points = 1.400000 m= 28442 mr = 55903 m= 4100 mr = 20956 m= 196 mr = 2532 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1957 time to turn everything in is 0.4000000 number of dielectric boundary points 32829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20429 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) : 0.6373760 object centre at (A) : 12.45750 -1.602500 17.52600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8856913E-02 6.3060727E-03 midg,1,midg; midg,igrid,midg -1.2379959E-02 2.6587827E-02 1,midg,midg; igrid,midg,midg -7.6535828E-03 5.2598856E-02 gauss-seidel spectral radius is 0.9986573 estimated iterations to convergence 216 setup time was (sec) 0.6200000 now iterating at: 04:29:59 rms-change max change #iterations 4.433798 182.4504 at 10iterations 2.090505 76.32387 at 20iterations 0.9891227 31.26732 at 30iterations 0.4669969 15.10297 at 40iterations 0.2199400 6.898191 at 50iterations 0.1039638 3.233963 at 60iterations 4.9006544E-02 1.452922 at 70iterations 2.3223601E-02 0.7845516 at 80iterations 1.0969843E-02 0.3528051 at 90iterations 5.1702182E-03 0.1651907 at 100iterations 2.4497064E-03 7.2301865E-02 at 110iterations 1.1587362E-03 4.0042877E-02 at 120iterations finished qdiffx linear iterations at : 04:30:06 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 1.1587362E-03 4.0042877E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 04:30:07 7.984u 0.186s 0:08.84 92.3% 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 04:30:07 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 = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.868192 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): -11.66700 36.58200 ymin,ymax (A): -25.74800 22.54300 zmin,zma (A): -10.40100 45.45300 x,y,z range (A): 48.24900 48.29100 55.85400 scale (grids/A): 2.868192 object centre (A): 12.45750 -1.602500 17.52600 number of atom coordinates read : 2744 total number of charged atoms : 2596 net assigned charge : 3.500012 assigned positive charge : 416.1166 centred at (gu) : 90.69844 91.79352 99.05598 assigned negative charge : -412.6172 centred at (gu) : 89.57402 91.03399 98.85535 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23168 grid for indexing accessible points = 1.400000 m= 92982 mr = 135021 m= 32709 mr = 76425 m= 7273 mr = 26185 m= 891 mr = 5363 m= 43 mr = 569 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 6890 time to turn everything in is 1.000000 number of dielectric boundary points 74079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 20766 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) : 1.912128 object centre at (A) : 12.45750 -1.602500 17.52600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5542834 0.3143944 midg,1,midg; midg,igrid,midg -0.1393542 0.3003094 1,midg,midg; igrid,midg,midg -2.8880242E-02 0.4570808 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 291 setup time was (sec) 1.240000 now iterating at: 04:30:09 rms-change max change #iterations 10.32810 377.5380 at 10iterations 6.028918 130.9958 at 20iterations 3.513147 80.60231 at 30iterations 2.041787 43.23703 at 40iterations 1.182992 21.90317 at 50iterations 0.6845722 12.42377 at 60iterations 0.3954474 7.178289 at 70iterations 0.2285607 4.067621 at 80iterations 0.1320675 2.298499 at 90iterations 7.6358072E-02 1.415213 at 100iterations 4.3981310E-02 0.8646102 at 110iterations 2.5400577E-02 0.4477015 at 120iterations 1.4617358E-02 0.2555943 at 130iterations 8.4447125E-03 0.1472398 at 140iterations 4.8919404E-03 8.8379860E-02 at 150iterations 2.8354474E-03 5.2360535E-02 at 160iterations 1.6499313E-03 2.9937983E-02 at 170iterations 9.6623227E-04 1.7680168E-02 at 180iterations finished qdiffx linear iterations at : 04:30:20 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 9.6623227E-04 1.7680168E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 04:30:21 12.809u 0.211s 0:13.41 97.0% 0+0k 0+0io 0pf+0w