Sun Oct 9 11:50:53 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 Sun Oct 9 2011 at 11:50:53 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 = 2747 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6706352 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): -4.628000 47.87900 ymin,ymax (A): 9.092000 60.33200 zmin,zma (A): 4.487000 57.57100 x,y,z range (A): 52.50700 51.24000 53.08400 scale (grids/A): 0.6706352 object centre (A): 21.62550 34.71200 31.02900 number of atom coordinates read : 2747 total number of charged atoms : 2675 net assigned charge : 2.500009 assigned positive charge : 410.5970 centred at (gu) : 90.72499 89.97807 91.63132 assigned negative charge : -408.0986 centred at (gu) : 90.78918 89.93542 91.56892 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8870 nv = 96 ne = 84 npr = 52296 no. pairs analyzed = 52296 no. exposed pairs = 3841 no. arc points = 27531 no. surface atoms = 1277 nbur = 1470 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 575 mr = 4579 m= 6 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2493 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 10121 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1472920E-09 3.5172267E-08 midg,1,midg; midg,igrid,midg -3.3855345E-09 1.9685203E-08 1,midg,midg; igrid,midg,midg 2.2028740E-08 -1.0889171E-08 gauss-seidel spectral radius is 0.9885093 estimated iterations to convergence 76 setup time was (sec) 0.5300000 now iterating at: 11:50:54 rms-change max change #iterations 0.1814816 23.83135 at 10iterations 1.9953471E-02 3.049346 at 20iterations 2.1870129E-03 0.2758694 at 30iterations 2.4077056E-04 3.4770966E-02 at 40iterations 3.1001939E-05 4.1818619E-03 at 50iterations finished qdiffx linear iterations at : 11:50:56 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 3.1001939E-05 4.1818619E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 11:50:57 3.166u 0.178s 0:03.63 91.7% 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 Sun Oct 9 2011 at 11:50:57 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 = 2747 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.011906 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): -4.628000 47.87900 ymin,ymax (A): 9.092000 60.33200 zmin,zma (A): 4.487000 57.57100 x,y,z range (A): 52.50700 51.24000 53.08400 scale (grids/A): 2.011906 object centre (A): 21.62550 34.71200 31.02900 number of atom coordinates read : 2747 total number of charged atoms : 2675 net assigned charge : 2.500009 assigned positive charge : 410.5970 centred at (gu) : 92.17398 89.93343 94.89331 assigned negative charge : -408.0986 centred at (gu) : 92.36764 89.80610 94.70690 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 93553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27531 grid for indexing accessible points = 1.400000 m= 35907 mr = 62660 m= 7578 mr = 25824 m= 741 mr = 4952 m= 18 mr = 352 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 44009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 21211 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) : 0.6706352 object centre at (A) : 21.62550 34.71200 31.02900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4205378E-03 5.0787885E-02 midg,1,midg; midg,igrid,midg -1.5190005E-02 3.2711435E-02 1,midg,midg; igrid,midg,midg 5.1196315E-04 -6.3164847E-04 gauss-seidel spectral radius is 0.9988156 estimated iterations to convergence 230 setup time was (sec) 0.9100000 now iterating at: 11:50:58 rms-change max change #iterations 4.873354 220.7636 at 10iterations 2.392243 82.31804 at 20iterations 1.173958 35.01224 at 30iterations 0.5798936 16.44690 at 40iterations 0.2855547 7.949686 at 50iterations 0.1406959 4.184273 at 60iterations 6.9148377E-02 2.113007 at 70iterations 3.4181423E-02 0.9470825 at 80iterations 1.6820375E-02 0.4729428 at 90iterations 8.3134770E-03 0.2468309 at 100iterations 4.0880125E-03 0.1267533 at 110iterations 2.0200894E-03 5.4958344E-02 at 120iterations finished qdiffx linear iterations at : 11:51:04 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 2.0200894E-03 5.4958344E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 11:51:04 7.194u 0.176s 0:07.69 95.7% 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 Sun Oct 9 2011 at 11:51:05 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 = 2747 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.017859 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): -4.628000 47.87900 ymin,ymax (A): 9.092000 60.33200 zmin,zma (A): 4.487000 57.57100 x,y,z range (A): 52.50700 51.24000 53.08400 scale (grids/A): 3.017859 object centre (A): 21.62550 34.71200 31.02900 number of atom coordinates read : 2747 total number of charged atoms : 2675 net assigned charge : 2.500009 assigned positive charge : 410.5970 centred at (gu) : 93.26077 89.89990 97.33979 assigned negative charge : -408.0986 centred at (gu) : 93.55141 89.70900 97.06020 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 215699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27531 grid for indexing accessible points = 1.400000 m= 110282 mr = 151985 m= 46149 mr = 88305 m= 14387 mr = 36856 m= 3058 mr = 11049 m= 343 mr = 2259 m= 12 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 99282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 21400 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) : 2.011906 object centre at (A) : 21.62550 34.71200 31.02900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6735237E-02 0.5786377 midg,1,midg; midg,igrid,midg -0.1062887 0.3988514 1,midg,midg; igrid,midg,midg -5.1169481E-02 0.3006249 gauss-seidel spectral radius is 0.9993331 estimated iterations to convergence 305 setup time was (sec) 1.950000 now iterating at: 11:51:07 rms-change max change #iterations 11.35512 428.2405 at 10iterations 6.924422 139.6583 at 20iterations 4.198440 89.63467 at 30iterations 2.531789 57.56158 at 40iterations 1.520661 27.63148 at 50iterations 0.9105282 15.18391 at 60iterations 0.5442772 9.706732 at 70iterations 0.3234706 5.884777 at 80iterations 0.1927122 3.253022 at 90iterations 0.1145824 1.947006 at 100iterations 6.8175018E-02 1.095034 at 110iterations 4.0318117E-02 0.6502542 at 120iterations 2.3962755E-02 0.3954248 at 130iterations 1.4192306E-02 0.2351902 at 140iterations 8.4101250E-03 0.1482849 at 150iterations 4.9851686E-03 8.3377838E-02 at 160iterations 2.9582474E-03 4.9060822E-02 at 170iterations 1.7467065E-03 2.9026031E-02 at 180iterations finished qdiffx linear iterations at : 11:51:17 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 1.7467065E-03 2.9026031E-02 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 11:51:17 12.152u 0.200s 0:12.64 97.7% 0+0k 0+0io 0pf+0w