Mon Oct 10 14:38:00 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 Mon Oct 10 2011 at 14:38:00 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 !!! WARNING: GLM 99 has a net charge of -0.0940 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: 0.5256552 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): -9.534000 47.42100 ymin,ymax (A): -16.75300 35.52200 zmin,zma (A): -24.88800 42.83700 x,y,z range (A): 56.95500 52.27500 67.72501 scale (grids/A): 0.5256552 object centre (A): 18.94350 9.384500 8.974501 number of atom coordinates read : 3103 total number of charged atoms : 2963 net assigned charge : 1.406008 assigned positive charge : 470.8599 centred at (gu) : 88.59547 88.06562 90.55809 assigned negative charge : -469.4551 centred at (gu) : 88.48604 88.11102 90.43169 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5590 nv = 96 ne = 84 npr = 60904 no. pairs analyzed = 60904 no. exposed pairs = 4272 no. arc points = 29644 no. surface atoms = 1431 nbur = 1672 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 254 mr = 2704 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2934 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7355 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1803352E-10 4.9902171E-10 midg,1,midg; midg,igrid,midg 3.0013927E-10 -6.3873948E-11 1,midg,midg; igrid,midg,midg -4.5332066E-10 2.6450722E-10 gauss-seidel spectral radius is 0.9813739 estimated iterations to convergence 60 setup time was (sec) 0.4200000 now iterating at: 14:38:01 rms-change max change #iterations 6.2325351E-02 10.82375 at 10iterations 4.2378348E-03 0.7351875 at 20iterations 4.6620652E-04 8.9351654E-02 at 30iterations 8.9169211E-05 1.6963959E-02 at 40iterations 1.9135154E-05 3.5972595E-03 at 50iterations finished qdiffx linear iterations at : 14:38:04 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.9135154E-05 3.5972595E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:38:04 3.454u 0.166s 0:04.15 86.9% 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 !!! WARNING: GLM 99 has a net charge of -0.0940 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: 1.576966 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): -9.534000 47.42100 ymin,ymax (A): -16.75300 35.52200 zmin,zma (A): -24.88800 42.83700 x,y,z range (A): 56.95500 52.27500 67.72501 scale (grids/A): 1.576966 object centre (A): 18.94350 9.384500 8.974501 number of atom coordinates read : 3103 total number of charged atoms : 2963 net assigned charge : 1.406008 assigned positive charge : 470.8599 centred at (gu) : 85.78582 84.19579 91.67349 assigned negative charge : -469.4551 centred at (gu) : 85.45767 84.33253 91.29459 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 61958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29644 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 18806 mr = 40312 m= 2033 mr = 12254 m= 61 mr = 919 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 29373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 22410 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) : 0.5256552 object centre at (A) : 18.94350 9.384500 8.974501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4866999E-03 2.7667519E-02 midg,1,midg; midg,igrid,midg 2.3308340E-03 -7.2105564E-03 1,midg,midg; igrid,midg,midg -1.0489033E-02 1.0364890E-03 gauss-seidel spectral radius is 0.9980675 estimated iterations to convergence 181 setup time was (sec) 0.5300000 now iterating at: 14:38:05 rms-change max change #iterations 3.147189 168.8481 at 10iterations 1.275050 58.46605 at 20iterations 0.5152202 19.67717 at 30iterations 0.2083231 9.147060 at 40iterations 8.4798753E-02 3.022700 at 50iterations 3.4545776E-02 1.275208 at 60iterations 1.4056126E-02 0.4862251 at 70iterations 5.7388921E-03 0.2185574 at 80iterations 2.3682262E-03 8.8830948E-02 at 90iterations 9.9328149E-04 4.5087814E-02 at 100iterations 4.2798469E-04 1.6681671E-02 at 110iterations 1.9165210E-04 7.2574615E-03 at 120iterations finished qdiffx linear iterations at : 14:38:12 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.9165210E-04 7.2574615E-03 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 14:38:13 7.724u 0.221s 0:08.44 94.0% 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 Mon Oct 10 2011 at 14:38:13 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 !!! WARNING: GLM 99 has a net charge of -0.0940 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: 2.365448 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): -9.534000 47.42100 ymin,ymax (A): -16.75300 35.52200 zmin,zma (A): -24.88800 42.83700 x,y,z range (A): 56.95500 52.27500 67.72501 scale (grids/A): 2.365448 object centre (A): 18.94350 9.384500 8.974501 number of atom coordinates read : 3103 total number of charged atoms : 2963 net assigned charge : 1.406008 assigned positive charge : 470.8599 centred at (gu) : 83.67850 81.29352 92.51003 assigned negative charge : -469.4551 centred at (gu) : 83.18645 81.49876 91.94177 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 144016 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29644 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 64816 mr = 99654 m= 18767 mr = 49644 m= 3025 mr = 13264 m= 188 mr = 1840 m= 5 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 66356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 23653 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) : 1.576966 object centre at (A) : 18.94350 9.384500 8.974501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3904580E-02 0.4914030 midg,1,midg; midg,igrid,midg 5.0824620E-02 -0.1330947 1,midg,midg; igrid,midg,midg -0.1643946 3.9530434E-03 gauss-seidel spectral radius is 0.9991017 estimated iterations to convergence 264 setup time was (sec) 1.000000 now iterating at: 14:38:14 rms-change max change #iterations 8.510401 362.8555 at 10iterations 4.774200 144.3643 at 20iterations 2.661852 65.51105 at 30iterations 1.474627 42.84786 at 40iterations 0.8109255 19.36830 at 50iterations 0.4451259 10.14040 at 60iterations 0.2431620 5.809870 at 70iterations 0.1327509 3.268131 at 80iterations 7.2580300E-02 1.522438 at 90iterations 3.9484877E-02 0.9081135 at 100iterations 2.1476641E-02 0.4776459 at 110iterations 1.1716867E-02 0.2697830 at 120iterations 6.3686157E-03 0.1449785 at 130iterations 3.4628643E-03 9.7716510E-02 at 140iterations 1.8854904E-03 4.1126251E-02 at 150iterations 1.0277486E-03 2.2600174E-02 at 160iterations 5.6327553E-04 1.1548996E-02 at 170iterations 3.1000510E-04 7.1506500E-03 at 180iterations finished qdiffx linear iterations at : 14:38:25 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 3.1000510E-04 7.1506500E-03 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 14:38:26 12.321u 0.206s 0:12.97 96.5% 0+0k 0+0io 0pf+0w