Sat Oct 8 17:09:13 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 17:09:13 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5188673 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): -14.18100 44.44600 ymin,ymax (A): -39.43100 29.18000 zmin,zma (A): -16.82800 35.41100 x,y,z range (A): 58.62700 68.61100 52.23901 scale (grids/A): 0.5188673 object centre (A): 15.13250 -5.125500 9.291501 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -4.499979 assigned positive charge : 529.9741 centred at (gu) : 90.43539 92.13681 90.62139 assigned negative charge : -534.4759 centred at (gu) : 90.45194 92.13550 90.57188 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5902 nv = 96 ne = 84 npr = 70979 no. pairs analyzed = 70979 no. exposed pairs = 4333 no. arc points = 30181 no. surface atoms = 1459 nbur = 2023 mkacc time = 0.2300000 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 = 1.680000 m= 205 mr = 3059 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3004 ## 461 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 7967 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9437281E-10 5.0666388E-11 midg,1,midg; midg,igrid,midg -5.6125968E-11 -1.5251213E-10 1,midg,midg; igrid,midg,midg -4.2289935E-11 -1.5359157E-10 gauss-seidel spectral radius is 0.9809052 estimated iterations to convergence 60 setup time was (sec) 0.7600000 now iterating at: 17:09:14 rms-change max change #iterations 6.2542565E-02 10.87228 at 10iterations 3.7473883E-03 0.5601239 at 20iterations 3.1810100E-04 5.1855564E-02 at 30iterations 6.5734901E-05 1.3067245E-02 at 40iterations 1.7518969E-05 3.5305023E-03 at 50iterations finished qdiffx linear iterations at : 17:09:18 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 1.7518969E-05 3.5305023E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 17:09:18 4.641u 0.431s 0:05.34 94.9% 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 17:09:18 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.556602 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): -14.18100 44.44600 ymin,ymax (A): -39.43100 29.18000 zmin,zma (A): -16.82800 35.41100 x,y,z range (A): 58.62700 68.61100 52.23901 scale (grids/A): 1.556602 object centre (A): 15.13250 -5.125500 9.291501 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -4.499979 assigned positive charge : 529.9741 centred at (gu) : 91.30488 96.40952 91.86349 assigned negative charge : -534.4759 centred at (gu) : 91.35551 96.40629 91.71527 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 66970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30181 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19905 mr = 46152 m= 1711 mr = 13401 m= 31 mr = 745 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 392 time to turn everything in is 0.7300000 number of dielectric boundary points 28319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 25233 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) : 0.5188673 object centre at (A) : 15.13250 -5.125500 9.291501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1980234E-03 1.8004950E-03 midg,1,midg; midg,igrid,midg 9.9749500E-03 1.3848549E-03 1,midg,midg; igrid,midg,midg -3.7822863E-03 -1.1214913E-02 gauss-seidel spectral radius is 0.9980368 estimated iterations to convergence 179 setup time was (sec) 1.070000 now iterating at: 17:09:20 rms-change max change #iterations 3.300368 147.5049 at 10iterations 1.331098 50.22418 at 20iterations 0.5363562 20.85059 at 30iterations 0.2167498 8.903778 at 40iterations 8.7387733E-02 3.030591 at 50iterations 3.5200946E-02 1.319929 at 60iterations 1.4136602E-02 0.5055180 at 70iterations 5.7360446E-03 0.1981182 at 80iterations 2.3153615E-03 8.3198547E-02 at 90iterations 9.4230875E-04 3.6508560E-02 at 100iterations 3.8389655E-04 1.3579369E-02 at 110iterations 1.5920447E-04 5.6648254E-03 at 120iterations finished qdiffx linear iterations at : 17:09:31 total time elapsed so far: 12.53000 # loops : 120 mean,max change (kT/e) : 1.5920447E-04 5.6648254E-03 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 17:09:32 12.760u 0.469s 0:13.59 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 Sat Oct 8 2011 at 17:09:32 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.334903 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): -14.18100 44.44600 ymin,ymax (A): -39.43100 29.18000 zmin,zma (A): -16.82800 35.41100 x,y,z range (A): 58.62700 68.61100 52.23901 scale (grids/A): 2.334903 object centre (A): 15.13250 -5.125500 9.291501 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -4.499979 assigned positive charge : 529.9741 centred at (gu) : 91.95709 99.61407 92.79506 assigned negative charge : -534.4759 centred at (gu) : 92.03313 99.60934 92.57289 start vw surface at 0.1900000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 155924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30181 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70850 mr = 112904 m= 18159 mr = 55821 m= 2528 mr = 13275 m= 150 mr = 1581 m= 0 mr = 42 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 1252 time to turn everything in is 1.770000 number of dielectric boundary points 63988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 26634 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) : 1.556602 object centre at (A) : 15.13250 -5.125500 9.291501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1087560 3.0758534E-02 midg,1,midg; midg,igrid,midg 0.4018772 4.0260544E-03 1,midg,midg; igrid,midg,midg -4.9559459E-02 -0.1514292 gauss-seidel spectral radius is 0.9990966 estimated iterations to convergence 263 setup time was (sec) 2.150000 now iterating at: 17:09:34 rms-change max change #iterations 8.718291 249.4972 at 10iterations 4.815102 114.9802 at 20iterations 2.640178 59.30513 at 30iterations 1.443819 40.64204 at 40iterations 0.7873114 18.99997 at 50iterations 0.4284174 10.62759 at 60iterations 0.2328510 4.986063 at 70iterations 0.1264275 2.538127 at 80iterations 6.8844825E-02 1.369568 at 90iterations 3.7258867E-02 0.8409958 at 100iterations 2.0171236E-02 0.4061170 at 110iterations 1.0959252E-02 0.2132583 at 120iterations 5.9458497E-03 0.1367383 at 130iterations 3.2279771E-03 7.0942879E-02 at 140iterations 1.7474267E-03 3.9550781E-02 at 150iterations 9.5288811E-04 2.0265579E-02 at 160iterations 5.1992165E-04 1.1356354E-02 at 170iterations 2.8515203E-04 5.8135986E-03 at 180iterations finished qdiffx linear iterations at : 17:09:50 total time elapsed so far: 17.98000 # loops : 180 mean,max change (kT/e) : 2.8515203E-04 5.8135986E-03 energy calculations done at 17.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.19000 DelPhi exited at 17:09:51 18.195u 0.499s 0:18.98 98.4% 0+0k 0+0io 0pf+0w