Tue Oct 11 03:24:25 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 Tue Oct 11 2011 at 03:24:25 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1174 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7451596 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): -6.781000 29.14500 ymin,ymax (A): 1.174000 41.15700 zmin,zma (A): -1.587000 46.18800 x,y,z range (A): 35.92600 39.98300 47.77500 scale (grids/A): 0.7451596 object centre (A): 11.18200 21.16550 22.30050 number of atom coordinates read : 1174 total number of charged atoms : 1052 net assigned charge : 5.514003 assigned positive charge : 177.7951 centred at (gu) : 90.02494 88.75037 88.37177 assigned negative charge : -172.2811 centred at (gu) : 89.73280 88.73335 88.36983 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4561 nv = 96 ne = 84 npr = 22810 no. pairs analyzed = 22810 no. exposed pairs = 1525 no. arc points = 11273 no. surface atoms = 512 nbur = 662 mkacc time = 3.0000001E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 284 mr = 2374 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 3.0000001E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.1200000 number of dielectric boundary points 2427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 917 ## 76 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4521 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4413915E-07 8.2232873E-08 midg,1,midg; midg,igrid,midg 1.2292843E-07 9.5080814E-08 1,midg,midg; igrid,midg,midg -7.2687556E-08 2.8170592E-07 gauss-seidel spectral radius is 0.9905196 estimated iterations to convergence 83 setup time was (sec) 0.3100000 now iterating at: 03:24:25 rms-change max change #iterations 0.1851436 28.93242 at 10iterations 2.4964413E-02 4.582798 at 20iterations 3.3420757E-03 0.6140461 at 30iterations 4.4232534E-04 6.8313599E-02 at 40iterations 5.9661761E-05 9.8419189E-03 at 50iterations finished qdiffx linear iterations at : 03:24:28 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 5.9661761E-05 9.8419189E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 03:24:29 3.259u 0.157s 0:03.98 85.4% 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 Tue Oct 11 2011 at 03:24:29 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1174 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.235479 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): -6.781000 29.14500 ymin,ymax (A): 1.174000 41.15700 zmin,zma (A): -1.587000 46.18800 x,y,z range (A): 35.92600 39.98300 47.77500 scale (grids/A): 2.235479 object centre (A): 11.18200 21.16550 22.30050 number of atom coordinates read : 1174 total number of charged atoms : 1052 net assigned charge : 5.514003 assigned positive charge : 177.7951 centred at (gu) : 90.07494 86.25119 85.11545 assigned negative charge : -172.2811 centred at (gu) : 89.19855 86.20027 85.10962 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 47024 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11273 grid for indexing accessible points = 1.400000 m= 17895 mr = 30641 m= 3536 mr = 13430 m= 366 mr = 2342 m= 10 mr = 192 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 900 time to turn everything in is 0.2600000 number of dielectric boundary points 22222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8396 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) : 0.7451596 object centre at (A) : 11.18200 21.16550 22.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1380705E-02 1.4504604E-02 midg,1,midg; midg,igrid,midg 4.2019710E-02 3.1433281E-02 1,midg,midg; igrid,midg,midg -2.2111664E-02 4.6495099E-02 gauss-seidel spectral radius is 0.9988497 estimated iterations to convergence 233 setup time was (sec) 0.4600000 now iterating at: 03:24:30 rms-change max change #iterations 3.754049 249.3006 at 10iterations 1.863141 87.27400 at 20iterations 0.9274020 35.25955 at 30iterations 0.4604841 17.76236 at 40iterations 0.2294702 9.622250 at 50iterations 0.1143072 4.340832 at 60iterations 5.6602061E-02 1.994237 at 70iterations 2.8139945E-02 1.029754 at 80iterations 1.4035777E-02 0.5842099 at 90iterations 6.9445674E-03 0.2448311 at 100iterations 3.4492533E-03 0.1176567 at 110iterations 1.7179583E-03 6.9763929E-02 at 120iterations finished qdiffx linear iterations at : 03:24:36 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 1.7179583E-03 6.9763929E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 03:24:37 7.463u 0.187s 0:08.11 94.2% 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 Tue Oct 11 2011 at 03:24:37 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1174 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.353218 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): -6.781000 29.14500 ymin,ymax (A): 1.174000 41.15700 zmin,zma (A): -1.587000 46.18800 x,y,z range (A): 35.92600 39.98300 47.77500 scale (grids/A): 3.353218 object centre (A): 11.18200 21.16550 22.30050 number of atom coordinates read : 1174 total number of charged atoms : 1052 net assigned charge : 5.514003 assigned positive charge : 177.7951 centred at (gu) : 90.11241 84.37679 82.67316 assigned negative charge : -172.2811 centred at (gu) : 88.79781 84.30048 82.66444 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 107941 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11273 grid for indexing accessible points = 1.400000 m= 54980 mr = 74007 m= 23049 mr = 44940 m= 6654 mr = 18904 m= 1418 mr = 5100 m= 207 mr = 1052 m= 20 mr = 149 m= 0 mr = 20 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2638 time to turn everything in is 0.7300000 number of dielectric boundary points 50097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 8416 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) : 2.235479 object centre at (A) : 11.18200 21.16550 22.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1863567 9.8791763E-02 midg,1,midg; midg,igrid,midg 0.3744423 0.2791271 1,midg,midg; igrid,midg,midg -0.1718095 0.3328041 gauss-seidel spectral radius is 0.9992966 estimated iterations to convergence 297 setup time was (sec) 0.9500000 now iterating at: 03:24:38 rms-change max change #iterations 8.144282 307.9675 at 10iterations 4.750652 125.7425 at 20iterations 2.754453 64.50403 at 30iterations 1.596589 36.53680 at 40iterations 0.9267296 21.23560 at 50iterations 0.5383158 10.70176 at 60iterations 0.3117001 6.679470 at 70iterations 0.1812701 3.655128 at 80iterations 0.1052786 2.291208 at 90iterations 6.0867034E-02 1.318905 at 100iterations 3.5345718E-02 0.7485704 at 110iterations 2.0559562E-02 0.4193296 at 120iterations 1.1926567E-02 0.2696686 at 130iterations 6.9193784E-03 0.1501617 at 140iterations 4.0136743E-03 7.9452515E-02 at 150iterations 2.3324327E-03 5.0683022E-02 at 160iterations 1.3524087E-03 2.9388428E-02 at 170iterations 7.8711571E-04 1.6361237E-02 at 180iterations finished qdiffx linear iterations at : 03:24:49 total time elapsed so far: 11.69000 # loops : 180 mean,max change (kT/e) : 7.8711571E-04 1.6361237E-02 energy calculations done at 11.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 03:24:50 11.818u 0.222s 0:12.42 96.8% 0+0k 0+0io 0pf+0w