Tue Oct 11 07:18:52 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 07:18:52 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3301 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5987419 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): 0.3019999 48.42800 ymin,ymax (A): -8.468000 48.41400 zmin,zma (A): 1.256000 60.71400 x,y,z range (A): 48.12600 56.88200 59.45800 scale (grids/A): 0.5987419 object centre (A): 24.36500 19.97300 30.98500 number of atom coordinates read : 3301 total number of charged atoms : 3150 net assigned charge : 9.6261501E-06 assigned positive charge : 495.7666 centred at (gu) : 89.94679 89.85142 90.61549 assigned negative charge : -495.7679 centred at (gu) : 89.87638 89.81502 90.57700 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7745 nv = 96 ne = 84 npr = 68093 no. pairs analyzed = 68093 no. exposed pairs = 3831 no. arc points = 26215 no. surface atoms = 1296 nbur = 2005 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 4504 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3800000 number of dielectric boundary points 3570 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2709 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9819 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5094596E-09 1.9765132E-09 midg,1,midg; midg,igrid,midg -1.7027733E-09 1.5648265E-09 1,midg,midg; igrid,midg,midg -3.2289191E-09 3.0878389E-09 gauss-seidel spectral radius is 0.9856160 estimated iterations to convergence 68 setup time was (sec) 0.6300000 now iterating at: 07:18:52 rms-change max change #iterations 0.1215260 19.32005 at 10iterations 1.0612675E-02 1.584110 at 20iterations 1.0080611E-03 0.1381149 at 30iterations 1.2845974E-04 2.3082733E-02 at 40iterations 2.3050110E-05 4.5471191E-03 at 50iterations finished qdiffx linear iterations at : 07:18:55 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 2.3050110E-05 4.5471191E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 07:18:56 3.640u 0.189s 0:04.16 91.8% 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 07:18:56 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3301 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: 1.796226 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): 0.3019999 48.42800 ymin,ymax (A): -8.468000 48.41400 zmin,zma (A): 1.256000 60.71400 x,y,z range (A): 48.12600 56.88200 59.45800 scale (grids/A): 1.796226 object centre (A): 24.36500 19.97300 30.98500 number of atom coordinates read : 3301 total number of charged atoms : 3150 net assigned charge : 9.6261501E-06 assigned positive charge : 495.7666 centred at (gu) : 89.83947 89.55351 91.84559 assigned negative charge : -495.7679 centred at (gu) : 89.62895 89.44466 91.73013 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26215 grid for indexing accessible points = 1.400000 m= 29777 mr = 61237 m= 4001 mr = 22486 m= 188 mr = 2515 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3523 time to turn everything in is 0.6200000 number of dielectric boundary points 32848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 24585 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) : 0.5987419 object centre at (A) : 24.36500 19.97300 30.98500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7692405E-03 8.9257630E-03 midg,1,midg; midg,igrid,midg -1.4512327E-02 1.9522525E-03 1,midg,midg; igrid,midg,midg -6.0434039E-03 1.9208720E-03 gauss-seidel spectral radius is 0.9985346 estimated iterations to convergence 207 setup time was (sec) 0.9300000 now iterating at: 07:18:57 rms-change max change #iterations 4.341173 200.2205 at 10iterations 1.973923 60.11440 at 20iterations 0.8991796 26.96587 at 30iterations 0.4114492 13.04061 at 40iterations 0.1879284 6.190819 at 50iterations 8.5996255E-02 2.622602 at 60iterations 3.9345812E-02 1.174675 at 70iterations 1.7934859E-02 0.5112305 at 80iterations 8.1879608E-03 0.2412834 at 90iterations 3.7400788E-03 0.1226444 at 100iterations 1.7111385E-03 5.6698799E-02 at 110iterations 7.8473153E-04 2.3691177E-02 at 120iterations finished qdiffx linear iterations at : 07:19:04 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 7.8473153E-04 2.3691177E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 07:19:04 8.095u 0.215s 0:08.59 96.6% 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 07:19:05 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3301 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: 2.694339 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): 0.3019999 48.42800 ymin,ymax (A): -8.468000 48.41400 zmin,zma (A): 1.256000 60.71400 x,y,z range (A): 48.12600 56.88200 59.45800 scale (grids/A): 2.694339 object centre (A): 24.36500 19.97300 30.98500 number of atom coordinates read : 3301 total number of charged atoms : 3150 net assigned charge : 9.6261501E-06 assigned positive charge : 495.7666 centred at (gu) : 89.75896 89.33012 92.76829 assigned negative charge : -495.7679 centred at (gu) : 89.44333 89.16687 92.59516 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 197700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26215 grid for indexing accessible points = 1.400000 m= 99456 mr = 148334 m= 33042 mr = 82677 m= 6959 mr = 26977 m= 830 mr = 5289 m= 47 mr = 576 m= 0 mr = 26 time to grow re-entrant surface = 0.8999999 no. cavity mid-points inaccessible to solvent = 12031 time to turn everything in is 1.590000 number of dielectric boundary points 74155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 25196 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) : 1.796226 object centre at (A) : 24.36500 19.97300 30.98500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1476476 -3.5608452E-02 midg,1,midg; midg,igrid,midg -0.2065575 1.6626267E-02 1,midg,midg; igrid,midg,midg -6.5363102E-02 2.7363107E-03 gauss-seidel spectral radius is 0.9992388 estimated iterations to convergence 286 setup time was (sec) 1.930000 now iterating at: 07:19:07 rms-change max change #iterations 10.34298 280.4807 at 10iterations 5.972317 138.5746 at 20iterations 3.430315 99.25890 at 30iterations 1.959156 35.11543 at 40iterations 1.123589 22.44496 at 50iterations 0.6426355 11.75211 at 60iterations 0.3670873 7.220854 at 70iterations 0.2092807 3.683743 at 80iterations 0.1194654 2.144691 at 90iterations 6.8233147E-02 1.108126 at 100iterations 3.8934827E-02 0.6578255 at 110iterations 2.2172481E-02 0.4087830 at 120iterations 1.2655529E-02 0.2213049 at 130iterations 7.2273547E-03 0.1364136 at 140iterations 4.1254056E-03 6.7546844E-02 at 150iterations 2.3679626E-03 3.9511681E-02 at 160iterations 1.3654764E-03 2.4749756E-02 at 170iterations 7.8850065E-04 1.4370203E-02 at 180iterations finished qdiffx linear iterations at : 07:19:18 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 7.8850065E-04 1.4370203E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 07:19:18 13.255u 0.235s 0:13.97 96.4% 0+0k 0+0io 0pf+0w