Sun Oct 9 15:27:26 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 Sun Oct 9 2011 at 15:27:26 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 = 5500 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4584557 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): 8.424999 63.41800 ymin,ymax (A): 53.43900 131.0910 zmin,zma (A): 29.32100 96.30900 x,y,z range (A): 54.99300 77.65199 66.98800 scale (grids/A): 0.4584557 object centre (A): 35.92150 92.26499 62.81500 number of atom coordinates read : 5500 total number of charged atoms : 5335 net assigned charge : 4.000029 assigned positive charge : 855.7562 centred at (gu) : 89.26200 89.43897 90.61001 assigned negative charge : -851.7639 centred at (gu) : 89.28227 89.38211 90.51806 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 6783 nv = 96 ne = 84 npr = 111368 no. pairs analyzed = 111368 no. exposed pairs = 6640 no. arc points = 46239 no. surface atoms = 2234 nbur = 3266 mkacc time = 0.3100000 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 = 1.876000 m= 199 mr = 3427 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 3555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4133 ## 807 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 9466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6611091E-11 3.3042222E-11 midg,1,midg; midg,igrid,midg -1.2604988E-11 1.5909211E-11 1,midg,midg; igrid,midg,midg 1.1646494E-11 -8.4181723E-13 gauss-seidel spectral radius is 0.9757454 estimated iterations to convergence 53 setup time was (sec) 0.8700000 now iterating at: 15:27:27 rms-change max change #iterations 4.1404378E-02 7.508106 at 10iterations 2.3563185E-03 0.3197556 at 20iterations 5.1585335E-04 6.5361977E-02 at 30iterations 1.6319711E-04 2.4552345E-02 at 40iterations 5.3170577E-05 8.7797642E-03 at 50iterations finished qdiffx linear iterations at : 15:27:30 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 5.3170577E-05 8.7797642E-03 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 15:27:31 4.398u 0.273s 0:04.95 94.1% 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 Sun Oct 9 2011 at 15:27:31 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 = 5500 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.375367 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): 8.424999 63.41800 ymin,ymax (A): 53.43900 131.0910 zmin,zma (A): 29.32100 96.30900 x,y,z range (A): 54.99300 77.65199 66.98800 scale (grids/A): 1.375367 object centre (A): 35.92150 92.26499 62.81500 number of atom coordinates read : 5500 total number of charged atoms : 5335 net assigned charge : 4.000029 assigned positive charge : 855.7562 centred at (gu) : 87.78480 88.31504 91.82813 assigned negative charge : -851.7639 centred at (gu) : 87.84681 88.14633 91.55355 start vw surface at 0.2300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 79273 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46239 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 19740 mr = 53933 m= 1145 mr = 12391 m= 12 mr = 331 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1093 time to turn everything in is 0.7500000 number of dielectric boundary points 33515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 847 ## 27 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 38360 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) : 0.4584557 object centre at (A) : 35.92150 92.26499 62.81500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3532449E-03 4.6861209E-03 midg,1,midg; midg,igrid,midg -2.8819062E-03 8.3409464E-03 1,midg,midg; igrid,midg,midg 5.1023951E-04 2.6254068E-04 gauss-seidel spectral radius is 0.9976440 estimated iterations to convergence 164 setup time was (sec) 1.050000 now iterating at: 15:27:32 rms-change max change #iterations 3.199239 130.1722 at 10iterations 1.178986 56.33427 at 20iterations 0.4351996 15.47851 at 30iterations 0.1617115 5.561134 at 40iterations 5.9841841E-02 2.242030 at 50iterations 2.2319660E-02 0.7758827 at 60iterations 8.3356593E-03 0.3491225 at 70iterations 3.2016928E-03 0.1221845 at 80iterations 1.3043393E-03 4.7859192E-02 at 90iterations 5.9930666E-04 1.9741058E-02 at 100iterations 3.2575618E-04 1.0639191E-02 at 110iterations 1.9882819E-04 6.7052841E-03 at 120iterations finished qdiffx linear iterations at : 15:27:41 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 1.9882819E-04 6.7052841E-03 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 15:27:41 9.547u 0.298s 0:10.10 97.3% 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 Sun Oct 9 2011 at 15:27:41 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 = 5500 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.063051 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): 8.424999 63.41800 ymin,ymax (A): 53.43900 131.0910 zmin,zma (A): 29.32100 96.30900 x,y,z range (A): 54.99300 77.65199 66.98800 scale (grids/A): 2.063051 object centre (A): 35.92150 92.26499 62.81500 number of atom coordinates read : 5500 total number of charged atoms : 5335 net assigned charge : 4.000029 assigned positive charge : 855.7562 centred at (gu) : 86.67694 87.47217 92.74182 assigned negative charge : -851.7639 centred at (gu) : 86.77001 87.21937 92.33031 start vw surface at 0.2400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 186314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46239 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 74993 mr = 134204 m= 14778 mr = 57048 m= 1395 mr = 9927 m= 25 mr = 651 m= 0 mr = 1 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 3444 time to turn everything in is 1.760000 number of dielectric boundary points 75674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 42262 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) : 1.375367 object centre at (A) : 35.92150 92.26499 62.81500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1944640E-02 4.4630725E-02 midg,1,midg; midg,igrid,midg -0.1019382 0.1531414 1,midg,midg; igrid,midg,midg 1.0466962E-02 1.7083630E-02 gauss-seidel spectral radius is 0.9990227 estimated iterations to convergence 253 setup time was (sec) 2.100000 now iterating at: 15:27:43 rms-change max change #iterations 9.392618 339.6791 at 10iterations 5.118119 127.7920 at 20iterations 2.775036 70.36021 at 30iterations 1.494850 37.97219 at 40iterations 0.8027013 19.53831 at 50iterations 0.4295192 9.761822 at 60iterations 0.2293222 5.252184 at 70iterations 0.1221293 2.764186 at 80iterations 6.5030865E-02 1.450834 at 90iterations 3.4616433E-02 0.8448162 at 100iterations 1.8414073E-02 0.3654008 at 110iterations 9.7796172E-03 0.1950489 at 120iterations 5.1931576E-03 0.1128254 at 130iterations 2.7645528E-03 5.5778503E-02 at 140iterations 1.4773264E-03 3.1223774E-02 at 150iterations 7.9975184E-04 1.6851425E-02 at 160iterations 4.3868722E-04 1.0358810E-02 at 170iterations 2.4885146E-04 5.9106350E-03 at 180iterations finished qdiffx linear iterations at : 15:27:57 total time elapsed so far: 15.87000 # loops : 180 mean,max change (kT/e) : 2.4885146E-04 5.9106350E-03 energy calculations done at 15.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.04000 DelPhi exited at 15:27:58 16.041u 0.307s 0:16.68 97.9% 0+0k 0+0io 0pf+0w