Mon Oct 10 22:03:56 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 22:03:57 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 = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5541028 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): -54.28600 9.962000 ymin,ymax (A): 32.48500 86.13600 zmin,zma (A): -17.35100 25.25300 x,y,z range (A): 64.24800 53.65100 42.60400 scale (grids/A): 0.5541028 object centre (A): -22.16200 59.31050 3.951000 number of atom coordinates read : 2673 total number of charged atoms : 2531 net assigned charge : 6.500013 assigned positive charge : 403.0027 centred at (gu) : 91.53476 89.55843 90.05545 assigned negative charge : -396.5034 centred at (gu) : 91.44415 89.65902 89.90802 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5246 nv = 96 ne = 84 npr = 54659 no. pairs analyzed = 54659 no. exposed pairs = 3070 no. arc points = 21235 no. surface atoms = 1043 nbur = 1630 mkacc time = 0.1200000 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 = 1.540000 m= 189 mr = 2902 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2800000 number of dielectric boundary points 2525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2107 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6765 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5194034E-10 1.7150625E-09 midg,1,midg; midg,igrid,midg 1.4808739E-09 -2.4466409E-10 1,midg,midg; igrid,midg,midg -1.2630344E-10 1.8246769E-09 gauss-seidel spectral radius is 0.9831711 estimated iterations to convergence 63 setup time was (sec) 0.5600000 now iterating at: 22:03:57 rms-change max change #iterations 7.7620156E-02 12.90702 at 10iterations 6.2600519E-03 1.275887 at 20iterations 8.8004948E-04 0.2298508 at 30iterations 1.9443916E-04 5.4103851E-02 at 40iterations 4.6269583E-05 1.2950897E-02 at 50iterations finished qdiffx linear iterations at : 22:04:01 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 4.6269583E-05 1.2950897E-02 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 22:04:01 4.217u 0.255s 0:04.80 92.9% 0+0k 0+0io 5pf+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 22:04:01 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 = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.662309 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): -54.28600 9.962000 ymin,ymax (A): 32.48500 86.13600 zmin,zma (A): -17.35100 25.25300 x,y,z range (A): 64.24800 53.65100 42.60400 scale (grids/A): 1.662309 object centre (A): -22.16200 59.31050 3.951000 number of atom coordinates read : 2673 total number of charged atoms : 2531 net assigned charge : 6.500013 assigned positive charge : 403.0027 centred at (gu) : 94.60376 88.67443 90.16605 assigned negative charge : -396.5034 centred at (gu) : 94.33204 88.97691 89.72366 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21235 grid for indexing accessible points = 1.400000 m= 18060 mr = 41128 m= 1769 mr = 13005 m= 39 mr = 929 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 0.4400000 number of dielectric boundary points 23356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 19458 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) : 0.5541028 object centre at (A) : -22.16200 59.31050 3.951000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4417777E-03 1.5242758E-02 midg,1,midg; midg,igrid,midg 1.5641896E-02 -2.7310385E-03 1,midg,midg; igrid,midg,midg -5.4715254E-04 -1.0196264E-02 gauss-seidel spectral radius is 0.9982065 estimated iterations to convergence 188 setup time was (sec) 0.7700000 now iterating at: 22:04:02 rms-change max change #iterations 3.260597 145.4543 at 10iterations 1.364450 52.94664 at 20iterations 0.5721222 23.26657 at 30iterations 0.2408682 9.627151 at 40iterations 0.1006811 3.547661 at 50iterations 4.2737626E-02 1.663507 at 60iterations 1.8100949E-02 0.7334518 at 70iterations 7.7189491E-03 0.3153410 at 80iterations 3.4433703E-03 0.1494484 at 90iterations 1.5974801E-03 7.3986053E-02 at 100iterations 7.9106860E-04 3.7055969E-02 at 110iterations 4.2203913E-04 2.1480560E-02 at 120iterations finished qdiffx linear iterations at : 22:04:11 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 4.2203913E-04 2.1480560E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 22:04:11 9.458u 0.288s 0:10.01 97.2% 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 22:04:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.493463 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): -54.28600 9.962000 ymin,ymax (A): 32.48500 86.13600 zmin,zma (A): -17.35100 25.25300 x,y,z range (A): 64.24800 53.65100 42.60400 scale (grids/A): 2.493463 object centre (A): -22.16200 59.31050 3.951000 number of atom coordinates read : 2673 total number of charged atoms : 2531 net assigned charge : 6.500013 assigned positive charge : 403.0027 centred at (gu) : 96.90538 88.01151 90.24894 assigned negative charge : -396.5034 centred at (gu) : 96.49804 88.46516 89.58553 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 136243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21235 grid for indexing accessible points = 1.400000 m= 63378 mr = 100243 m= 17800 mr = 51622 m= 2732 mr = 13715 m= 144 mr = 1912 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2113 time to turn everything in is 1.040000 number of dielectric boundary points 52754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 20234 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) : 1.662309 object centre at (A) : -22.16200 59.31050 3.951000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9755432E-02 0.2029561 midg,1,midg; midg,igrid,midg 0.1812267 -6.7841463E-02 1,midg,midg; igrid,midg,midg -7.9319440E-02 -0.1523764 gauss-seidel spectral radius is 0.9991279 estimated iterations to convergence 268 setup time was (sec) 1.390000 now iterating at: 22:04:13 rms-change max change #iterations 8.149929 258.4285 at 10iterations 4.486073 104.9686 at 20iterations 2.475435 58.35726 at 30iterations 1.356438 32.50800 at 40iterations 0.7467223 16.36565 at 50iterations 0.4090031 8.597548 at 60iterations 0.2239067 4.942842 at 70iterations 0.1225349 2.588007 at 80iterations 6.7159154E-02 1.475626 at 90iterations 3.6867246E-02 0.7439880 at 100iterations 2.0268179E-02 0.4587631 at 110iterations 1.1156718E-02 0.2446442 at 120iterations 6.1910716E-03 0.1381836 at 130iterations 3.4700881E-03 8.2927704E-02 at 140iterations 1.9812116E-03 4.6524048E-02 at 150iterations 1.1656914E-03 3.4099579E-02 at 160iterations 7.1238127E-04 2.1045685E-02 at 170iterations 4.5721489E-04 1.3710022E-02 at 180iterations finished qdiffx linear iterations at : 22:04:27 total time elapsed so far: 14.79000 # loops : 180 mean,max change (kT/e) : 4.5721489E-04 1.3710022E-02 energy calculations done at 14.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.97000 DelPhi exited at 22:04:27 14.970u 0.299s 0:15.80 96.5% 0+0k 0+0io 0pf+0w