Mon Oct 10 17:13:21 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 17:13:21 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2381 !!! WARNING: HIR 129 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5659688 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): -26.43100 36.47000 ymin,ymax (A): -4.064000 37.81300 zmin,zma (A): 26.17900 80.77600 x,y,z range (A): 62.90100 41.87700 54.59700 scale (grids/A): 0.5659688 object centre (A): 5.019499 16.87450 53.47750 number of atom coordinates read : 2381 total number of charged atoms : 2249 net assigned charge : -7.985983 assigned positive charge : 345.0724 centred at (gu) : 88.74232 89.69802 91.02020 assigned negative charge : -353.0586 centred at (gu) : 88.67075 89.72298 91.04516 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5015 nv = 96 ne = 84 npr = 48858 no. pairs analyzed = 48858 no. exposed pairs = 3230 no. arc points = 23641 no. surface atoms = 1091 nbur = 1290 mkacc time = 0.1100000 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= 192 mr = 2341 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2600000 number of dielectric boundary points 2858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2314 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6407 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1340416E-10 -1.6700634E-09 midg,1,midg; midg,igrid,midg -8.2780138E-10 -1.2235283E-09 1,midg,midg; igrid,midg,midg -2.4623770E-09 -2.1366420E-10 gauss-seidel spectral radius is 0.9838543 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 17:13:22 rms-change max change #iterations 8.1291370E-02 15.05780 at 10iterations 5.8109933E-03 0.9791832 at 20iterations 4.2324248E-04 8.0783844E-02 at 30iterations 3.1556843E-05 5.4798126E-03 at 40iterations 2.4205094E-06 4.1961670E-04 at 50iterations finished qdiffx linear iterations at : 17:13:25 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 2.4205094E-06 4.1961670E-04 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 17:13:26 4.317u 0.287s 0:04.90 93.6% 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 17:13:26 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2381 !!! WARNING: HIR 129 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.697906 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): -26.43100 36.47000 ymin,ymax (A): -4.064000 37.81300 zmin,zma (A): 26.17900 80.77600 x,y,z range (A): 62.90100 41.87700 54.59700 scale (grids/A): 1.697906 object centre (A): 5.019499 16.87450 53.47750 number of atom coordinates read : 2381 total number of charged atoms : 2249 net assigned charge : -7.985983 assigned positive charge : 345.0724 centred at (gu) : 86.22676 89.09386 93.06052 assigned negative charge : -353.0586 centred at (gu) : 86.01212 89.16875 93.13545 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 55324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23641 grid for indexing accessible points = 1.400000 m= 15392 mr = 35165 m= 1393 mr = 9893 m= 36 mr = 574 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1244 time to turn everything in is 0.4200000 number of dielectric boundary points 26513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 17418 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) : 0.5659688 object centre at (A) : 5.019499 16.87450 53.47750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7565259E-02 -1.2167813E-02 midg,1,midg; midg,igrid,midg -3.7339774E-03 -4.2049754E-03 1,midg,midg; igrid,midg,midg 4.8492504E-03 7.0981476E-03 gauss-seidel spectral radius is 0.9982698 estimated iterations to convergence 191 setup time was (sec) 0.7300000 now iterating at: 17:13:27 rms-change max change #iterations 3.177269 190.0115 at 10iterations 1.348985 62.54394 at 20iterations 0.5716820 26.94320 at 30iterations 0.2438452 9.800678 at 40iterations 0.1033163 3.781782 at 50iterations 4.3981075E-02 1.650892 at 60iterations 1.8608810E-02 0.7275772 at 70iterations 7.9179602E-03 0.3262062 at 80iterations 3.3727905E-03 0.1456261 at 90iterations 1.4294276E-03 5.9989214E-02 at 100iterations 6.0821709E-04 2.4009705E-02 at 110iterations 2.5810971E-04 1.0374069E-02 at 120iterations finished qdiffx linear iterations at : 17:13:35 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 2.5810971E-04 1.0374069E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 17:13:36 9.274u 0.275s 0:09.89 96.4% 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 17:13:36 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2381 !!! WARNING: HIR 129 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.546860 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): -26.43100 36.47000 ymin,ymax (A): -4.064000 37.81300 zmin,zma (A): 26.17900 80.77600 x,y,z range (A): 62.90100 41.87700 54.59700 scale (grids/A): 2.546860 object centre (A): 5.019499 16.87450 53.47750 number of atom coordinates read : 2381 total number of charged atoms : 2249 net assigned charge : -7.985983 assigned positive charge : 345.0724 centred at (gu) : 84.33995 88.64072 94.59056 assigned negative charge : -353.0586 centred at (gu) : 84.01812 88.75310 94.70303 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 128298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23641 grid for indexing accessible points = 1.400000 m= 53885 mr = 86520 m= 14083 mr = 40737 m= 2003 mr = 9984 m= 123 mr = 1232 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 4019 time to turn everything in is 1.010000 number of dielectric boundary points 59870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 17983 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) : 1.697906 object centre at (A) : 5.019499 16.87450 53.47750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3576536 -0.1722166 midg,1,midg; midg,igrid,midg -3.8287945E-02 -4.2322848E-02 1,midg,midg; igrid,midg,midg -0.1164713 8.2977101E-02 gauss-seidel spectral radius is 0.9991607 estimated iterations to convergence 273 setup time was (sec) 1.350000 now iterating at: 17:13:37 rms-change max change #iterations 8.080606 309.7570 at 10iterations 4.591214 142.8370 at 20iterations 2.584593 84.37192 at 30iterations 1.448293 38.27375 at 40iterations 0.8085473 19.26937 at 50iterations 0.4514714 10.09321 at 60iterations 0.2509913 5.960724 at 70iterations 0.1395471 3.279518 at 80iterations 7.7399306E-02 1.890106 at 90iterations 4.3023054E-02 1.079088 at 100iterations 2.3873303E-02 0.6126903 at 110iterations 1.3204739E-02 0.2982898 at 120iterations 7.2975941E-03 0.1556702 at 130iterations 4.0382426E-03 8.8104248E-02 at 140iterations 2.2360657E-03 5.7041168E-02 at 150iterations 1.2372581E-03 2.8182983E-02 at 160iterations 6.8356638E-04 1.6186714E-02 at 170iterations 3.7858964E-04 8.4495544E-03 at 180iterations finished qdiffx linear iterations at : 17:13:51 total time elapsed so far: 14.66000 # loops : 180 mean,max change (kT/e) : 3.7858964E-04 8.4495544E-03 energy calculations done at 14.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.83000 DelPhi exited at 17:13:51 14.835u 0.262s 0:15.38 98.1% 0+0k 0+0io 0pf+0w