Mon Oct 10 14:37:49 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 14:37:49 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 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: 0.6241344 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): -2.616000 44.15300 ymin,ymax (A): 3.798000 60.83700 zmin,zma (A): -16.40400 36.80400 x,y,z range (A): 46.76900 57.03900 53.20800 scale (grids/A): 0.6241344 object centre (A): 20.76850 32.31750 10.20000 number of atom coordinates read : 2253 total number of charged atoms : 2099 net assigned charge : 5.3495169E-06 assigned positive charge : 325.4765 centred at (gu) : 89.12751 89.92550 90.46836 assigned negative charge : -325.4768 centred at (gu) : 89.01058 90.06000 90.52187 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6049 nv = 96 ne = 84 npr = 45194 no. pairs analyzed = 45194 no. exposed pairs = 3067 no. arc points = 21740 no. surface atoms = 1022 nbur = 1231 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3059 m= 0 mr = 26 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2089 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0930158E-09 -3.6471417E-09 midg,1,midg; midg,igrid,midg 8.5506802E-09 -8.3342258E-09 1,midg,midg; igrid,midg,midg -8.9297654E-09 6.0457932E-09 gauss-seidel spectral radius is 0.9866836 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 14:37:50 rms-change max change #iterations 0.1159513 19.27580 at 10iterations 1.0837053E-02 2.096954 at 20iterations 1.0027412E-03 0.1433239 at 30iterations 9.2036469E-05 1.3027191E-02 at 40iterations 8.6750524E-06 1.6231537E-03 at 50iterations finished qdiffx linear iterations at : 14:37:53 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 8.6750524E-06 1.6231537E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:37:54 4.022u 0.279s 0:04.86 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 Mon Oct 10 2011 at 14:37:54 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 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: 1.872403 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): -2.616000 44.15300 ymin,ymax (A): 3.798000 60.83700 zmin,zma (A): -16.40400 36.80400 x,y,z range (A): 46.76900 57.03900 53.20800 scale (grids/A): 1.872403 object centre (A): 20.76850 32.31750 10.20000 number of atom coordinates read : 2253 total number of charged atoms : 2099 net assigned charge : 5.3495169E-06 assigned positive charge : 325.4765 centred at (gu) : 87.38208 89.77614 91.40459 assigned negative charge : -325.4768 centred at (gu) : 87.03165 90.17992 91.56551 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 65115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21740 grid for indexing accessible points = 1.400000 m= 22251 mr = 43305 m= 3091 mr = 15522 m= 186 mr = 1653 m= 4 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 30109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 16484 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) : 0.6241344 object centre at (A) : 20.76850 32.31750 10.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6531707E-03 -1.6466102E-02 midg,1,midg; midg,igrid,midg 7.3838299E-03 2.6311965E-03 1,midg,midg; igrid,midg,midg -4.0250500E-03 6.2258816E-03 gauss-seidel spectral radius is 0.9985642 estimated iterations to convergence 209 setup time was (sec) 0.9100000 now iterating at: 14:37:55 rms-change max change #iterations 3.702651 166.9693 at 10iterations 1.695980 73.94270 at 20iterations 0.7737253 29.90609 at 30iterations 0.3558038 11.32610 at 40iterations 0.1624160 5.221606 at 50iterations 7.4544363E-02 2.548368 at 60iterations 3.4221273E-02 1.239491 at 70iterations 1.5682576E-02 0.6167126 at 80iterations 7.2049927E-03 0.2350044 at 90iterations 3.2994067E-03 0.1417122 at 100iterations 1.5115084E-03 5.0116658E-02 at 110iterations 6.9467805E-04 2.4080276E-02 at 120iterations finished qdiffx linear iterations at : 14:38:04 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 6.9467805E-04 2.4080276E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 14:38:04 9.302u 0.277s 0:10.23 93.5% 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 14:38:04 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 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: 2.808604 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): -2.616000 44.15300 ymin,ymax (A): 3.798000 60.83700 zmin,zma (A): -16.40400 36.80400 x,y,z range (A): 46.76900 57.03900 53.20800 scale (grids/A): 2.808604 object centre (A): 20.76850 32.31750 10.20000 number of atom coordinates read : 2253 total number of charged atoms : 2099 net assigned charge : 5.3495169E-06 assigned positive charge : 325.4765 centred at (gu) : 86.07301 89.66414 92.10682 assigned negative charge : -325.4768 centred at (gu) : 85.54732 90.26986 92.34825 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 150519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21740 grid for indexing accessible points = 1.400000 m= 72849 mr = 105386 m= 24889 mr = 57843 m= 5274 mr = 19079 m= 675 mr = 3543 m= 55 mr = 427 m= 0 mr = 30 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 67953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 16791 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) : 1.872403 object centre at (A) : 20.76850 32.31750 10.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8287929E-02 -0.2649995 midg,1,midg; midg,igrid,midg 1.4086952E-02 0.1374685 1,midg,midg; igrid,midg,midg 1.6126962E-02 2.9622821E-02 gauss-seidel spectral radius is 0.9992420 estimated iterations to convergence 287 setup time was (sec) 1.810000 now iterating at: 14:38:07 rms-change max change #iterations 8.924067 365.1861 at 10iterations 5.222243 136.6139 at 20iterations 3.019444 65.15307 at 30iterations 1.741256 38.48190 at 40iterations 1.002349 20.20822 at 50iterations 0.5749291 12.91069 at 60iterations 0.3296164 7.020813 at 70iterations 0.1886340 3.821836 at 80iterations 0.1079507 2.221024 at 90iterations 6.1545327E-02 1.326439 at 100iterations 3.5206530E-02 0.7825530 at 110iterations 2.0082688E-02 0.4348226 at 120iterations 1.1450045E-02 0.2316065 at 130iterations 6.5332442E-03 0.1212664 at 140iterations 3.7298677E-03 7.3644638E-02 at 150iterations 2.1252579E-03 4.1477203E-02 at 160iterations 1.2120779E-03 2.3028851E-02 at 170iterations 6.8945927E-04 1.4936447E-02 at 180iterations finished qdiffx linear iterations at : 14:38:20 total time elapsed so far: 15.25000 # loops : 180 mean,max change (kT/e) : 6.8945927E-04 1.4936447E-02 energy calculations done at 15.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.44000 DelPhi exited at 14:38:21 15.438u 0.306s 0:16.14 97.4% 0+0k 0+0io 0pf+0w