Mon Oct 10 13:58:12 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 Mon Oct 10 2011 at 13:58:12 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 448 has a net charge of 1.4000 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: 0.6206740 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): -31.75500 17.63600 ymin,ymax (A): -23.10000 23.50600 zmin,zma (A): -12.49300 44.86400 x,y,z range (A): 49.39100 46.60600 57.35700 scale (grids/A): 0.6206740 object centre (A): -7.059501 0.2030001 16.18550 number of atom coordinates read : 2559 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.51205 88.91382 89.78629 assigned negative charge : -387.4045 centred at (gu) : 88.42271 88.95991 89.65375 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6527 nv = 96 ne = 84 npr = 52572 no. pairs analyzed = 52572 no. exposed pairs = 2995 no. arc points = 21633 no. surface atoms = 1000 nbur = 1559 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3679 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2100000 number of dielectric boundary points 3153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2159 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8101 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9878587E-09 1.1611650E-08 midg,1,midg; midg,igrid,midg 8.2026546E-09 2.2703400E-10 1,midg,midg; igrid,midg,midg -3.8829002E-09 6.7453167E-09 gauss-seidel spectral radius is 0.9865497 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 13:58:12 rms-change max change #iterations 0.1259649 27.43387 at 10iterations 1.1616318E-02 1.982157 at 20iterations 1.0877382E-03 0.1620498 at 30iterations 1.0888805E-04 1.7139435E-02 at 40iterations 1.2149223E-05 2.3250580E-03 at 50iterations finished qdiffx linear iterations at : 13:58:15 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.2149223E-05 2.3250580E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 13:58:16 3.455u 0.154s 0:04.04 89.1% 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 13:58:16 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 448 has a net charge of 1.4000 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: 1.862022 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): -31.75500 17.63600 ymin,ymax (A): -23.10000 23.50600 zmin,zma (A): -12.49300 44.86400 x,y,z range (A): 49.39100 46.60600 57.35700 scale (grids/A): 1.862022 object centre (A): -7.059501 0.2030001 16.18550 number of atom coordinates read : 2559 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.53542 86.74079 89.35854 assigned negative charge : -387.4045 centred at (gu) : 85.26790 86.87964 88.96101 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21633 grid for indexing accessible points = 1.400000 m= 24637 mr = 49538 m= 3487 mr = 18189 m= 158 mr = 2076 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3631 time to turn everything in is 0.3400000 number of dielectric boundary points 29032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19253 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) : 0.6206740 object centre at (A) : -7.059501 0.2030001 16.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1870071E-02 2.5417373E-02 midg,1,midg; midg,igrid,midg 1.4348653E-02 1.2739679E-03 1,midg,midg; igrid,midg,midg -2.8640728E-03 2.8858634E-02 gauss-seidel spectral radius is 0.9985659 estimated iterations to convergence 209 setup time was (sec) 0.5400000 now iterating at: 13:58:16 rms-change max change #iterations 4.021592 189.0028 at 10iterations 1.857430 60.78273 at 20iterations 0.8485749 28.49005 at 30iterations 0.3902824 13.64866 at 40iterations 0.1800383 5.874390 at 50iterations 8.2893774E-02 2.896576 at 60iterations 3.7959691E-02 1.344276 at 70iterations 1.7428745E-02 0.5782166 at 80iterations 8.0366675E-03 0.2343826 at 90iterations 3.6998766E-03 0.1190224 at 100iterations 1.7022339E-03 5.5728912E-02 at 110iterations 7.8418269E-04 2.6526451E-02 at 120iterations finished qdiffx linear iterations at : 13:58:24 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 7.8418269E-04 2.6526451E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 13:58:24 7.827u 0.221s 0:08.62 93.2% 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 13:58:24 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 448 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.793033 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): -31.75500 17.63600 ymin,ymax (A): -23.10000 23.50600 zmin,zma (A): -12.49300 44.86400 x,y,z range (A): 49.39100 46.60600 57.35700 scale (grids/A): 2.793033 object centre (A): -7.059501 0.2030001 16.18550 number of atom coordinates read : 2559 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.30310 85.11118 89.03790 assigned negative charge : -387.4045 centred at (gu) : 82.90175 85.31939 88.44145 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21633 grid for indexing accessible points = 1.400000 m= 81381 mr = 119767 m= 27589 mr = 67049 m= 6118 mr = 22110 m= 662 mr = 4466 m= 30 mr = 387 m= 0 mr = 12 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 12085 time to turn everything in is 0.8700000 number of dielectric boundary points 65336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19629 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) : 1.862022 object centre at (A) : -7.059501 0.2030001 16.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1039953 0.2448082 midg,1,midg; midg,igrid,midg 0.1467634 -1.2997154E-02 1,midg,midg; igrid,midg,midg -4.3436554E-03 0.3818748 gauss-seidel spectral radius is 0.9992341 estimated iterations to convergence 285 setup time was (sec) 1.100000 now iterating at: 13:58:26 rms-change max change #iterations 9.467156 402.4501 at 10iterations 5.452737 125.0334 at 20iterations 3.116161 78.48628 at 30iterations 1.779624 42.03684 at 40iterations 1.017944 21.84275 at 50iterations 0.5785052 12.54835 at 60iterations 0.3310631 8.198198 at 70iterations 0.1879983 3.671341 at 80iterations 0.1070070 2.148748 at 90iterations 6.0911514E-02 1.219169 at 100iterations 3.4710765E-02 0.7366776 at 110iterations 1.9769076E-02 0.3699858 at 120iterations 1.1251122E-02 0.2201653 at 130iterations 6.3980687E-03 0.1221428 at 140iterations 3.6560472E-03 7.1404576E-02 at 150iterations 2.0861300E-03 3.8722992E-02 at 160iterations 1.1952844E-03 2.3921967E-02 at 170iterations 6.8704260E-04 1.3542175E-02 at 180iterations finished qdiffx linear iterations at : 13:58:37 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 6.8704260E-04 1.3542175E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 13:58:37 12.213u 0.194s 0:12.76 97.1% 0+0k 0+0io 0pf+0w