Tue Oct 11 07:32:27 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 Tue Oct 11 2011 at 07:32:28 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.6027360 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): 75.61400 125.7500 ymin,ymax (A): -8.717000 49.22800 zmin,zma (A): -2.340000 56.72400 x,y,z range (A): 50.13600 57.94500 59.06400 scale (grids/A): 0.6027360 object centre (A): 100.6820 20.25550 27.19200 number of atom coordinates read : 3315 total number of charged atoms : 3162 net assigned charge : -0.5999901 assigned positive charge : 497.7356 centred at (gu) : 90.63849 89.61707 89.11821 assigned negative charge : -498.3368 centred at (gu) : 90.74506 89.53979 89.16774 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7896 nv = 96 ne = 84 npr = 68851 no. pairs analyzed = 68851 no. exposed pairs = 3766 no. arc points = 25865 no. surface atoms = 1291 nbur = 2024 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 4630 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.4200000 number of dielectric boundary points 3594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2640 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7799079E-09 -2.2750068E-09 midg,1,midg; midg,igrid,midg -4.6041104E-09 3.3472412E-09 1,midg,midg; igrid,midg,midg 4.4182733E-09 -6.6510797E-09 gauss-seidel spectral radius is 0.9858039 estimated iterations to convergence 69 setup time was (sec) 0.6400000 now iterating at: 07:32:28 rms-change max change #iterations 0.1248896 17.71322 at 10iterations 1.1451098E-02 1.375420 at 20iterations 1.3663599E-03 0.2030525 at 30iterations 2.7441981E-04 4.2945862E-02 at 40iterations 7.1256283E-05 1.1369705E-02 at 50iterations finished qdiffx linear iterations at : 07:32:31 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.1256283E-05 1.1369705E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 07:32:32 3.455u 0.141s 0:04.07 88.2% 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 07:32:32 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.808208 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): 75.61400 125.7500 ymin,ymax (A): -8.717000 49.22800 zmin,zma (A): -2.340000 56.72400 x,y,z range (A): 50.13600 57.94500 59.06400 scale (grids/A): 1.808208 object centre (A): 100.6820 20.25550 27.19200 number of atom coordinates read : 3315 total number of charged atoms : 3162 net assigned charge : -0.5999901 assigned positive charge : 497.7356 centred at (gu) : 91.91453 88.85059 87.35362 assigned negative charge : -498.3368 centred at (gu) : 92.23499 88.61887 87.50279 start vw surface at 0.2700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 87220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25865 grid for indexing accessible points = 1.400000 m= 30839 mr = 63434 m= 3867 mr = 23074 m= 134 mr = 2256 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3001 time to turn everything in is 0.7300000 number of dielectric boundary points 33264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 24676 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) : 0.6027360 object centre at (A) : 100.6820 20.25550 27.19200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2151933E-03 -1.3320123E-02 midg,1,midg; midg,igrid,midg -1.1957977E-02 8.1943879E-03 1,midg,midg; igrid,midg,midg 1.6883016E-02 -1.4499994E-02 gauss-seidel spectral radius is 0.9985539 estimated iterations to convergence 208 setup time was (sec) 1.020000 now iterating at: 07:32:33 rms-change max change #iterations 4.387409 189.5349 at 10iterations 2.012531 64.07801 at 20iterations 0.9223672 28.45048 at 30iterations 0.4248376 12.02824 at 40iterations 0.1953071 5.687329 at 50iterations 8.9840114E-02 2.644098 at 60iterations 4.1503817E-02 1.411736 at 70iterations 1.9082889E-02 0.5715733 at 80iterations 8.8490872E-03 0.2569866 at 90iterations 4.1513834E-03 0.1236038 at 100iterations 1.9681084E-03 5.8944702E-02 at 110iterations 9.5952244E-04 3.1747818E-02 at 120iterations finished qdiffx linear iterations at : 07:32:39 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 9.5952244E-04 3.1747818E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 07:32:40 7.734u 0.155s 0:08.20 96.0% 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 07:32:40 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3315 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.712312 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): 75.61400 125.7500 ymin,ymax (A): -8.717000 49.22800 zmin,zma (A): -2.340000 56.72400 x,y,z range (A): 50.13600 57.94500 59.06400 scale (grids/A): 2.712312 object centre (A): 100.6820 20.25550 27.19200 number of atom coordinates read : 3315 total number of charged atoms : 3162 net assigned charge : -0.5999901 assigned positive charge : 497.7356 centred at (gu) : 92.87157 88.27562 86.03014 assigned negative charge : -498.3368 centred at (gu) : 93.35226 87.92823 86.25411 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 202182 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25865 grid for indexing accessible points = 1.400000 m= 102556 mr = 152804 m= 33837 mr = 85574 m= 6565 mr = 27177 m= 637 mr = 4784 m= 32 mr = 371 m= 0 mr = 16 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 10086 time to turn everything in is 1.630000 number of dielectric boundary points 75083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 25292 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) : 1.808208 object centre at (A) : 100.6820 20.25550 27.19200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2077537 -0.3944758 midg,1,midg; midg,igrid,midg 1.8358182E-02 9.3636639E-02 1,midg,midg; igrid,midg,midg 0.1882305 -0.1797555 gauss-seidel spectral radius is 0.9992446 estimated iterations to convergence 287 setup time was (sec) 1.970000 now iterating at: 07:32:42 rms-change max change #iterations 10.43820 303.1940 at 10iterations 6.078342 135.9324 at 20iterations 3.504037 66.11426 at 30iterations 2.015741 34.70715 at 40iterations 1.161198 25.27029 at 50iterations 0.6650483 11.47829 at 60iterations 0.3818165 6.931425 at 70iterations 0.2183457 3.764410 at 80iterations 0.1249735 2.267862 at 90iterations 7.1584590E-02 1.327238 at 100iterations 4.0967826E-02 0.7002001 at 110iterations 2.3478463E-02 0.4242306 at 120iterations 1.3436332E-02 0.2218084 at 130iterations 7.7355360E-03 0.1314716 at 140iterations 4.4745477E-03 8.6746216E-02 at 150iterations 2.6057556E-03 5.1403046E-02 at 160iterations 1.5476595E-03 2.7946472E-02 at 170iterations 9.3795516E-04 1.6370773E-02 at 180iterations finished qdiffx linear iterations at : 07:32:54 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 9.3795516E-04 1.6370773E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 07:32:54 13.647u 0.231s 0:14.36 96.5% 0+0k 0+0io 0pf+0w