Sun Oct 9 21:05:44 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 Sun Oct 9 2011 at 21:05:45 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 !!! WARNING: SEP 141 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5837022 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): -8.867001 49.73900 ymin,ymax (A): 23.17400 84.16400 zmin,zma (A): -5.057000 47.29400 x,y,z range (A): 58.60600 60.99000 52.35100 scale (grids/A): 0.5837022 object centre (A): 20.43600 53.66900 21.11850 number of atom coordinates read : 3194 total number of charged atoms : 3043 net assigned charge : 3.025009 assigned positive charge : 484.4518 centred at (gu) : 90.72024 89.26708 89.48240 assigned negative charge : -481.4280 centred at (gu) : 90.77778 89.16395 89.46027 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7225 nv = 96 ne = 84 npr = 62882 no. pairs analyzed = 62882 no. exposed pairs = 4010 no. arc points = 28992 no. surface atoms = 1342 nbur = 1852 mkacc time = 0.1400000 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 = 1.456000 m= 335 mr = 3793 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3200000 number of dielectric boundary points 3743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2909 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9150 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1450985E-10 1.2297180E-09 midg,1,midg; midg,igrid,midg -2.4107045E-09 2.9769345E-09 1,midg,midg; igrid,midg,midg 1.9701520E-09 -9.1879415E-10 gauss-seidel spectral radius is 0.9848717 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 21:05:45 rms-change max change #iterations 0.1096925 16.43414 at 10iterations 8.5448232E-03 1.480209 at 20iterations 6.8820984E-04 0.1170082 at 30iterations 5.8578502E-05 7.8315735E-03 at 40iterations 6.6347357E-06 9.0217590E-04 at 50iterations finished qdiffx linear iterations at : 21:05:48 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 6.6347357E-06 9.0217590E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 21:05:48 3.435u 0.198s 0:03.90 92.8% 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 Sun Oct 9 2011 at 21:05:49 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 1.751107 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): -8.867001 49.73900 ymin,ymax (A): 23.17400 84.16400 zmin,zma (A): -5.057000 47.29400 x,y,z range (A): 58.60600 60.99000 52.35100 scale (grids/A): 1.751107 object centre (A): 20.43600 53.66900 21.11850 number of atom coordinates read : 3194 total number of charged atoms : 3043 net assigned charge : 3.025009 assigned positive charge : 484.4518 centred at (gu) : 92.16029 87.80012 88.44694 assigned negative charge : -481.4280 centred at (gu) : 92.33285 87.49165 88.38069 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28992 grid for indexing accessible points = 1.400000 m= 25541 mr = 53561 m= 3368 mr = 17827 m= 158 mr = 1918 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1197 time to turn everything in is 0.5400000 number of dielectric boundary points 34591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 23657 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) : 0.5837022 object centre at (A) : 20.43600 53.66900 21.11850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8465508E-03 2.4626488E-03 midg,1,midg; midg,igrid,midg -1.4787107E-02 -1.4497370E-02 1,midg,midg; igrid,midg,midg -5.8127744E-03 3.1928727E-03 gauss-seidel spectral radius is 0.9984610 estimated iterations to convergence 202 setup time was (sec) 0.8300000 now iterating at: 21:05:50 rms-change max change #iterations 4.020619 180.0781 at 10iterations 1.781438 59.93375 at 20iterations 0.7942287 25.97923 at 30iterations 0.3552796 11.70584 at 40iterations 0.1583511 5.526571 at 50iterations 7.0837796E-02 2.226490 at 60iterations 3.1496502E-02 1.055801 at 70iterations 1.4078985E-02 0.4521885 at 80iterations 6.3092471E-03 0.1962423 at 90iterations 2.8170636E-03 9.0362549E-02 at 100iterations 1.2594848E-03 4.1469336E-02 at 110iterations 5.6399032E-04 1.7688751E-02 at 120iterations finished qdiffx linear iterations at : 21:05:56 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 5.6399032E-04 1.7688751E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 21:05:57 7.737u 0.256s 0:08.27 96.4% 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 21:05:57 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 2.626660 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): -8.867001 49.73900 ymin,ymax (A): 23.17400 84.16400 zmin,zma (A): -5.057000 47.29400 x,y,z range (A): 58.60600 60.99000 52.35100 scale (grids/A): 2.626660 object centre (A): 20.43600 53.66900 21.11850 number of atom coordinates read : 3194 total number of charged atoms : 3043 net assigned charge : 3.025009 assigned positive charge : 484.4518 centred at (gu) : 93.24012 86.69990 87.67017 assigned negative charge : -481.4280 centred at (gu) : 93.49923 86.23721 87.57100 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 183006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28992 grid for indexing accessible points = 1.400000 m= 85794 mr = 130922 m= 27118 mr = 68282 m= 5668 mr = 20708 m= 651 mr = 3952 m= 27 mr = 372 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 4042 time to turn everything in is 1.380000 number of dielectric boundary points 78026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 24330 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) : 1.751107 object centre at (A) : 20.43600 53.66900 21.11850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1091552 2.2891304E-02 midg,1,midg; midg,igrid,midg -0.2947438 -0.2775473 1,midg,midg; igrid,midg,midg -0.1988620 -7.0155233E-02 gauss-seidel spectral radius is 0.9992257 estimated iterations to convergence 284 setup time was (sec) 1.670000 now iterating at: 21:05:59 rms-change max change #iterations 9.989957 357.4592 at 10iterations 5.833485 142.9721 at 20iterations 3.359054 73.41959 at 30iterations 1.936519 40.05182 at 40iterations 1.108951 24.65575 at 50iterations 0.6352584 12.84752 at 60iterations 0.3631539 7.860022 at 70iterations 0.2069891 3.919096 at 80iterations 0.1179566 2.255165 at 90iterations 6.7239553E-02 1.288736 at 100iterations 3.8153522E-02 0.6873055 at 110iterations 2.1698399E-02 0.4734039 at 120iterations 1.2345321E-02 0.2096958 at 130iterations 6.9967862E-03 0.1452579 at 140iterations 3.9812075E-03 7.2475433E-02 at 150iterations 2.2599546E-03 4.3592453E-02 at 160iterations 1.2829732E-03 2.2451162E-02 at 170iterations 7.2946766E-04 1.3980865E-02 at 180iterations finished qdiffx linear iterations at : 21:06:08 total time elapsed so far: 11.04000 # loops : 180 mean,max change (kT/e) : 7.2946766E-04 1.3980865E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 21:06:09 11.266u 0.187s 0:11.72 97.6% 0+0k 0+0io 0pf+0w