Tue Oct 11 03:19:09 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 03:19:09 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 = 2982 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: 0.5950391 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): -37.77700 20.78300 ymin,ymax (A): -38.74500 19.77900 zmin,zma (A): -67.42300 -7.595000 x,y,z range (A): 58.56000 58.52400 59.82800 scale (grids/A): 0.5950391 object centre (A): -8.497001 -9.483001 -37.50900 number of atom coordinates read : 2982 total number of charged atoms : 2829 net assigned charge : -2.499985 assigned positive charge : 440.7292 centred at (gu) : 89.76807 87.97966 90.56496 assigned negative charge : -443.2303 centred at (gu) : 89.81988 88.01801 90.52718 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7310 nv = 96 ne = 84 npr = 57462 no. pairs analyzed = 57462 no. exposed pairs = 4243 no. arc points = 29866 no. surface atoms = 1409 nbur = 1573 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3621 m= 1 mr = 13 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 0.3400000 number of dielectric boundary points 4024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3069 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9003 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0197652E-09 4.4841469E-10 midg,1,midg; midg,igrid,midg 6.9053468E-10 -1.4689587E-09 1,midg,midg; igrid,midg,midg 9.3164265E-10 -2.6557931E-09 gauss-seidel spectral radius is 0.9854339 estimated iterations to convergence 68 setup time was (sec) 0.5500000 now iterating at: 03:19:10 rms-change max change #iterations 0.1074291 20.05993 at 10iterations 9.0142246E-03 1.590833 at 20iterations 7.4790226E-04 0.1198959 at 30iterations 6.7976733E-05 9.3123913E-03 at 40iterations 7.8043458E-06 1.1367798E-03 at 50iterations finished qdiffx linear iterations at : 03:19:12 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 7.8043458E-06 1.1367798E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 03:19:13 3.154u 0.134s 0:03.59 91.3% 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 03:19:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 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: 1.785117 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): -37.77700 20.78300 ymin,ymax (A): -38.74500 19.77900 zmin,zma (A): -67.42300 -7.595000 x,y,z range (A): 58.56000 58.52400 59.82800 scale (grids/A): 1.785117 object centre (A): -8.497001 -9.483001 -37.50900 number of atom coordinates read : 2982 total number of charged atoms : 2829 net assigned charge : -2.499985 assigned positive charge : 440.7292 centred at (gu) : 89.30361 83.93819 91.69408 assigned negative charge : -443.2303 centred at (gu) : 89.45930 84.05373 91.58109 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 79380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29866 grid for indexing accessible points = 1.400000 m= 26336 mr = 52380 m= 3366 mr = 17949 m= 146 mr = 1712 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 37158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22048 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) : 0.5950391 object centre at (A) : -8.497001 -9.483001 -37.50900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9959774E-02 -2.1484707E-02 midg,1,midg; midg,igrid,midg -7.5881206E-03 -3.9805882E-02 1,midg,midg; igrid,midg,midg 2.5355328E-02 -4.4753803E-03 gauss-seidel spectral radius is 0.9985108 estimated iterations to convergence 206 setup time was (sec) 0.9100000 now iterating at: 03:19:14 rms-change max change #iterations 4.028014 161.0429 at 10iterations 1.808529 69.54458 at 20iterations 0.8149448 29.30028 at 30iterations 0.3684238 12.07638 at 40iterations 0.1664681 5.783214 at 50iterations 7.5176150E-02 2.370572 at 60iterations 3.3933308E-02 1.213192 at 70iterations 1.5325418E-02 0.4892960 at 80iterations 6.9407001E-03 0.2283087 at 90iterations 3.1582876E-03 0.1091137 at 100iterations 1.4244108E-03 4.4937134E-02 at 110iterations 6.4514746E-04 2.0732820E-02 at 120iterations finished qdiffx linear iterations at : 03:19:20 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 6.4514746E-04 2.0732820E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 03:19:21 7.523u 0.181s 0:08.00 96.2% 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 03:19:21 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 = 2982 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.677676 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): -37.77700 20.78300 ymin,ymax (A): -38.74500 19.77900 zmin,zma (A): -67.42300 -7.595000 x,y,z range (A): 58.56000 58.52400 59.82800 scale (grids/A): 2.677676 object centre (A): -8.497001 -9.483001 -37.50900 number of atom coordinates read : 2982 total number of charged atoms : 2829 net assigned charge : -2.499985 assigned positive charge : 440.7292 centred at (gu) : 88.95516 80.90716 92.54086 assigned negative charge : -443.2303 centred at (gu) : 89.18882 81.08050 92.37169 start vw surface at 0.2400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 183800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29866 grid for indexing accessible points = 1.400000 m= 87379 mr = 128154 m= 28161 mr = 68438 m= 5506 mr = 21139 m= 569 mr = 3638 m= 31 mr = 289 m= 0 mr = 5 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 83783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 22629 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) : 1.785117 object centre at (A) : -8.497001 -9.483001 -37.50900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5304732 -0.2230215 midg,1,midg; midg,igrid,midg -3.1526305E-02 -0.7303613 1,midg,midg; igrid,midg,midg 0.2463056 -5.6533504E-02 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 1.760000 now iterating at: 03:19:23 rms-change max change #iterations 10.09434 357.3928 at 10iterations 6.020813 156.0949 at 20iterations 3.546022 83.21893 at 30iterations 2.067419 54.77218 at 40iterations 1.202907 22.90923 at 50iterations 0.6968615 15.36936 at 60iterations 0.4024557 7.326191 at 70iterations 0.2320534 4.510890 at 80iterations 0.1337638 2.527359 at 90iterations 7.6941893E-02 1.371913 at 100iterations 4.4165011E-02 0.8686218 at 110iterations 2.5356375E-02 0.4601727 at 120iterations 1.4529330E-02 0.2520618 at 130iterations 8.3489893E-03 0.1467113 at 140iterations 4.7788974E-03 9.5705032E-02 at 150iterations 2.7389908E-03 5.1850319E-02 at 160iterations 1.5750052E-03 3.1009674E-02 at 170iterations 9.0248778E-04 1.6586304E-02 at 180iterations finished qdiffx linear iterations at : 03:19:32 total time elapsed so far: 11.29000 # loops : 180 mean,max change (kT/e) : 9.0248778E-04 1.6586304E-02 energy calculations done at 11.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 03:19:33 11.464u 0.188s 0:12.00 97.0% 0+0k 0+0io 0pf+0w