Sat Oct 8 11:48:46 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 Sat Oct 8 2011 at 11:48:46 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2898 !!! WARNING: HIT 137 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: 0.5648821 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): -13.10700 42.12600 ymin,ymax (A): -13.77200 49.25000 zmin,zma (A): 20.95200 77.07100 x,y,z range (A): 55.23300 63.02200 56.11900 scale (grids/A): 0.5648821 object centre (A): 14.50950 17.73900 49.01150 number of atom coordinates read : 2898 total number of charged atoms : 2742 net assigned charge : -7.485985 assigned positive charge : 431.5049 centred at (gu) : 90.89719 92.23876 92.00903 assigned negative charge : -438.9919 centred at (gu) : 90.90657 92.19460 91.92950 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6145 nv = 96 ne = 84 npr = 56293 no. pairs analyzed = 56293 no. exposed pairs = 4079 no. arc points = 29973 no. surface atoms = 1358 nbur = 1540 mkacc time = 9.9999994E-02 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= 274 mr = 2871 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2946 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7860 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2511848E-09 9.2412092E-11 midg,1,midg; midg,igrid,midg -9.1710545E-10 -6.7629741E-10 1,midg,midg; igrid,midg,midg -6.9750916E-10 -1.3565323E-09 gauss-seidel spectral radius is 0.9838402 estimated iterations to convergence 65 setup time was (sec) 0.4200000 now iterating at: 11:48:47 rms-change max change #iterations 8.6808436E-02 14.87217 at 10iterations 6.3786185E-03 1.015465 at 20iterations 4.6630812E-04 8.2052231E-02 at 30iterations 3.6307647E-05 5.5522919E-03 at 40iterations 3.3843917E-06 4.9686432E-04 at 50iterations finished qdiffx linear iterations at : 11:48:50 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 3.3843917E-06 4.9686432E-04 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 11:48:50 3.648u 0.191s 0:04.14 92.5% 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 Sat Oct 8 2011 at 11:48:50 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2898 !!! WARNING: HIT 137 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: 1.694646 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): -13.10700 42.12600 ymin,ymax (A): -13.77200 49.25000 zmin,zma (A): 20.95200 77.07100 x,y,z range (A): 55.23300 63.02200 56.11900 scale (grids/A): 1.694646 object centre (A): 14.50950 17.73900 49.01150 number of atom coordinates read : 2898 total number of charged atoms : 2742 net assigned charge : -7.485985 assigned positive charge : 431.5049 centred at (gu) : 92.69054 96.71552 96.02586 assigned negative charge : -438.9919 centred at (gu) : 92.71906 96.58352 95.78783 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29973 grid for indexing accessible points = 1.400000 m= 19437 mr = 42702 m= 2111 mr = 12553 m= 78 mr = 958 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 32886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21172 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) : 0.5648821 object centre at (A) : 14.50950 17.73900 49.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7188284E-03 7.1323025E-03 midg,1,midg; midg,igrid,midg -2.1437760E-02 -5.2071367E-03 1,midg,midg; igrid,midg,midg -1.7747800E-03 -9.9237077E-03 gauss-seidel spectral radius is 0.9983281 estimated iterations to convergence 194 setup time was (sec) 0.5900000 now iterating at: 11:48:51 rms-change max change #iterations 3.597965 196.6236 at 10iterations 1.541999 68.37997 at 20iterations 0.6622850 24.07273 at 30iterations 0.2848884 9.487343 at 40iterations 0.1225401 4.308908 at 50iterations 5.2755859E-02 1.797466 at 60iterations 2.2747919E-02 0.7957649 at 70iterations 9.7800568E-03 0.3376083 at 80iterations 4.2209099E-03 0.1425228 at 90iterations 1.8199888E-03 7.2277069E-02 at 100iterations 7.8690669E-04 2.6784897E-02 at 110iterations 3.3881742E-04 1.2922287E-02 at 120iterations finished qdiffx linear iterations at : 11:48:59 total time elapsed so far: 8.430000 # loops : 120 mean,max change (kT/e) : 3.3881742E-04 1.2922287E-02 energy calculations done at 8.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.550000 DelPhi exited at 11:49:00 8.557u 0.245s 0:09.07 96.9% 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 Sat Oct 8 2011 at 11:49:00 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2898 !!! WARNING: HIT 137 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: 2.541970 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): -13.10700 42.12600 ymin,ymax (A): -13.77200 49.25000 zmin,zma (A): 20.95200 77.07100 x,y,z range (A): 55.23300 63.02200 56.11900 scale (grids/A): 2.541970 object centre (A): 14.50950 17.73900 49.01150 number of atom coordinates read : 2898 total number of charged atoms : 2742 net assigned charge : -7.485985 assigned positive charge : 431.5049 centred at (gu) : 94.03563 100.0731 99.03848 assigned negative charge : -438.9919 centred at (gu) : 94.07856 99.87494 98.68169 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 156597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29973 grid for indexing accessible points = 1.400000 m= 67070 mr = 105315 m= 18921 mr = 50786 m= 3257 mr = 13431 m= 336 mr = 2070 m= 5 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 74432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21922 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) : 1.694646 object centre at (A) : 14.50950 17.73900 49.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1281878E-03 0.1381946 midg,1,midg; midg,igrid,midg -0.1976254 -0.1163117 1,midg,midg; igrid,midg,midg 4.0679704E-02 -0.1679984 gauss-seidel spectral radius is 0.9991908 estimated iterations to convergence 278 setup time was (sec) 1.040000 now iterating at: 11:49:01 rms-change max change #iterations 9.088524 326.7640 at 10iterations 5.225770 158.2438 at 20iterations 2.983596 71.74576 at 30iterations 1.689199 38.55956 at 40iterations 0.9563733 20.21683 at 50iterations 0.5411119 11.73366 at 60iterations 0.3045579 6.264969 at 70iterations 0.1715098 3.808274 at 80iterations 9.6443549E-02 1.901134 at 90iterations 5.4180272E-02 1.085487 at 100iterations 3.0398259E-02 0.6166725 at 110iterations 1.7030766E-02 0.3693619 at 120iterations 9.5544206E-03 0.2233958 at 130iterations 5.3470791E-03 0.1071892 at 140iterations 2.9963553E-03 6.3282013E-02 at 150iterations 1.6796541E-03 3.2367706E-02 at 160iterations 9.4004656E-04 1.8898487E-02 at 170iterations 5.2620232E-04 1.0262966E-02 at 180iterations finished qdiffx linear iterations at : 11:49:14 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 5.2620232E-04 1.0262966E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 11:49:14 12.820u 0.230s 0:14.45 90.3% 0+0k 0+0io 0pf+0w