Wed Dec 28 11:03:34 PST 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 Wed Dec 28 2011 at 11:03:34 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1972 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5598276 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): -42.01200 3.666000 ymin,ymax (A): 13.78800 54.57500 zmin,zma (A): -4.486000 59.10500 x,y,z range (A): 45.67800 40.78700 63.59100 scale (grids/A): 0.5598276 object centre (A): -19.17300 34.18150 27.30950 number of atom coordinates read : 1972 total number of charged atoms : 1840 net assigned charge : 4.000004 assigned positive charge : 291.5840 centred at (gu) : 89.59635 90.11996 89.97380 assigned negative charge : -287.5843 centred at (gu) : 89.68326 89.97555 89.97665 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4088 nv = 96 ne = 84 npr = 40054 no. pairs analyzed = 40054 no. exposed pairs = 2492 no. arc points = 18009 no. surface atoms = 838 nbur = 1134 mkacc time = 0.1000000 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 = 1.568000 m= 142 mr = 2154 m= 1 mr = 12 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 0.2500000 number of dielectric boundary points 2065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1791 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 5192 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4289233E-10 3.9707002E-10 midg,1,midg; midg,igrid,midg -6.0957556E-10 1.4738417E-09 1,midg,midg; igrid,midg,midg 1.1389267E-09 -1.8517504E-10 gauss-seidel spectral radius is 0.9834602 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 11:03:35 rms-change max change #iterations 6.7399159E-02 15.90819 at 10iterations 4.8479447E-03 0.8945923 at 20iterations 3.3894327E-04 5.6957245E-02 at 30iterations 2.3563205E-05 4.2285919E-03 at 40iterations 1.7017103E-06 3.4523010E-04 at 50iterations finished qdiffx linear iterations at : 11:03:42 total time elapsed so far: 7.750000 # loops : 50 mean,max change (kT/e) : 1.7017103E-06 3.4523010E-04 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 11:03:43 7.933u 0.608s 0:08.98 94.9% 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 Wed Dec 28 2011 at 11:03:43 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1972 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.679483 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): -42.01200 3.666000 ymin,ymax (A): 13.78800 54.57500 zmin,zma (A): -4.486000 59.10500 x,y,z range (A): 45.67800 40.78700 63.59100 scale (grids/A): 1.679483 object centre (A): -19.17300 34.18150 27.30950 number of atom coordinates read : 1972 total number of charged atoms : 1840 net assigned charge : 4.000004 assigned positive charge : 291.5840 centred at (gu) : 88.78889 90.35995 89.92133 assigned negative charge : -287.5843 centred at (gu) : 89.04999 89.92695 89.93012 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 45109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18009 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14172 mr = 30433 m= 1428 mr = 10374 m= 41 mr = 716 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 612 time to turn everything in is 0.4500000 number of dielectric boundary points 19227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 14207 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) : 0.5598276 object centre at (A) : -19.17300 34.18150 27.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0982938E-02 2.0166332E-02 midg,1,midg; midg,igrid,midg -4.2810882E-03 2.9035562E-03 1,midg,midg; igrid,midg,midg -4.3403159E-04 -7.7993545E-04 gauss-seidel spectral radius is 0.9981673 estimated iterations to convergence 186 setup time was (sec) 0.9900000 now iterating at: 11:03:45 rms-change max change #iterations 2.761393 157.2957 at 10iterations 1.142342 49.20829 at 20iterations 0.4734283 19.53752 at 30iterations 0.1967084 8.829260 at 40iterations 8.1384987E-02 3.240967 at 50iterations 3.3868153E-02 1.370514 at 60iterations 1.4159173E-02 0.6882124 at 70iterations 5.8675208E-03 0.2417412 at 80iterations 2.4263384E-03 0.1040516 at 90iterations 1.0048993E-03 4.0400505E-02 at 100iterations 4.1900942E-04 1.6939163E-02 at 110iterations 1.7418894E-04 7.2021484E-03 at 120iterations finished qdiffx linear iterations at : 11:04:01 total time elapsed so far: 17.21000 # loops : 120 mean,max change (kT/e) : 1.7418894E-04 7.2021484E-03 energy calculations done at 17.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.38000 DelPhi exited at 11:04:02 17.382u 0.837s 0:18.75 97.1% 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 Wed Dec 28 2011 at 11:04:02 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1972 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.519224 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): -42.01200 3.666000 ymin,ymax (A): 13.78800 54.57500 zmin,zma (A): -4.486000 59.10500 x,y,z range (A): 45.67800 40.78700 63.59100 scale (grids/A): 2.519224 object centre (A): -19.17300 34.18150 27.30950 number of atom coordinates read : 1972 total number of charged atoms : 1840 net assigned charge : 4.000004 assigned positive charge : 291.5840 centred at (gu) : 88.18331 90.53989 89.88203 assigned negative charge : -287.5843 centred at (gu) : 88.57504 89.89049 89.89528 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 104542 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18009 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 49152 mr = 74103 m= 14316 mr = 40131 m= 2208 mr = 11288 m= 140 mr = 1421 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2225 time to turn everything in is 1.120000 number of dielectric boundary points 43363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 14704 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) : 1.679483 object centre at (A) : -19.17300 34.18150 27.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2076018 0.2017061 midg,1,midg; midg,igrid,midg -5.9548430E-02 9.1898972E-03 1,midg,midg; igrid,midg,midg -3.5448503E-02 -1.6808674E-02 gauss-seidel spectral radius is 0.9990982 estimated iterations to convergence 263 setup time was (sec) 1.710000 now iterating at: 11:04:04 rms-change max change #iterations 6.984724 361.9916 at 10iterations 3.807607 111.3868 at 20iterations 2.072011 64.08347 at 30iterations 1.125953 30.21954 at 40iterations 0.6099089 16.18093 at 50iterations 0.3295587 8.097519 at 60iterations 0.1783172 4.731241 at 70iterations 9.6374497E-02 2.226643 at 80iterations 5.2087829E-02 1.338048 at 90iterations 2.8152039E-02 0.6848221 at 100iterations 1.5202776E-02 0.3887405 at 110iterations 8.2200700E-03 0.2093029 at 120iterations 4.4495850E-03 0.1021423 at 130iterations 2.4049496E-03 6.1342239E-02 at 140iterations 1.3013334E-03 3.2149792E-02 at 150iterations 7.0144591E-04 1.6523361E-02 at 160iterations 3.7959134E-04 9.0560913E-03 at 170iterations 2.0468245E-04 4.9476624E-03 at 180iterations finished qdiffx linear iterations at : 11:04:32 total time elapsed so far: 29.27000 # loops : 180 mean,max change (kT/e) : 2.0468245E-04 4.9476624E-03 energy calculations done at 29.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.45000 DelPhi exited at 11:04:33 29.452u 0.815s 0:30.84 98.1% 0+0k 0+0io 0pf+0w