Sat Oct 8 16:59:37 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 Sat Oct 8 2011 at 16:59:37 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 = 3503 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: 0.5155908 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): -4.802000 64.24500 ymin,ymax (A): 15.13700 76.70900 zmin,zma (A): -13.21900 34.74600 x,y,z range (A): 69.04700 61.57200 47.96500 scale (grids/A): 0.5155908 object centre (A): 29.72150 45.92300 10.76350 number of atom coordinates read : 3503 total number of charged atoms : 3358 net assigned charge : -3.999995 assigned positive charge : 527.6923 centred at (gu) : 90.19702 87.23013 89.41331 assigned negative charge : -531.6938 centred at (gu) : 90.23460 87.29443 89.41724 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5820 nv = 96 ne = 84 npr = 72170 no. pairs analyzed = 72170 no. exposed pairs = 4246 no. arc points = 29338 no. surface atoms = 1434 nbur = 2069 mkacc time = 0.1800000 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 = 1.652000 m= 207 mr = 3074 m= 3 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 2948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2915 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7827 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5798645E-11 -7.2211660E-11 midg,1,midg; midg,igrid,midg 1.6521534E-10 -1.1163036E-10 1,midg,midg; igrid,midg,midg 1.2849077E-11 -1.7237370E-10 gauss-seidel spectral radius is 0.9806618 estimated iterations to convergence 59 setup time was (sec) 0.6700000 now iterating at: 16:59:38 rms-change max change #iterations 5.9511900E-02 14.77010 at 10iterations 3.4438008E-03 0.6058006 at 20iterations 2.1545384E-04 3.6963940E-02 at 30iterations 2.1878821E-05 5.4845810E-03 at 40iterations 4.6326932E-06 1.3217926E-03 at 50iterations finished qdiffx linear iterations at : 16:59:42 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 4.6326932E-06 1.3217926E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 16:59:43 4.675u 0.390s 0:05.36 94.4% 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 Sat Oct 8 2011 at 16:59:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 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: 1.546772 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): -4.802000 64.24500 ymin,ymax (A): 15.13700 76.70900 zmin,zma (A): -13.21900 34.74600 x,y,z range (A): 69.04700 61.57200 47.96500 scale (grids/A): 1.546772 object centre (A): 29.72150 45.92300 10.76350 number of atom coordinates read : 3503 total number of charged atoms : 3358 net assigned charge : -3.999995 assigned positive charge : 527.6923 centred at (gu) : 90.59026 81.68960 88.23901 assigned negative charge : -531.6938 centred at (gu) : 90.70336 81.88280 88.25110 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29338 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 18956 mr = 45333 m= 1618 mr = 12697 m= 28 mr = 743 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 27562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 444 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 25327 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) : 0.5155908 object centre at (A) : 29.72150 45.92300 10.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6785414E-04 -2.7632946E-04 midg,1,midg; midg,igrid,midg -1.3504202E-02 -1.0675220E-02 1,midg,midg; igrid,midg,midg 1.1419097E-02 -4.0329555E-03 gauss-seidel spectral radius is 0.9980025 estimated iterations to convergence 178 setup time was (sec) 0.8400000 now iterating at: 16:59:44 rms-change max change #iterations 3.204889 172.0321 at 10iterations 1.276584 48.87394 at 20iterations 0.5118084 19.30662 at 30iterations 0.2044631 8.668465 at 40iterations 8.1747323E-02 2.897385 at 50iterations 3.2704212E-02 1.158148 at 60iterations 1.3145327E-02 0.5021422 at 70iterations 5.2588065E-03 0.1944180 at 80iterations 2.1140517E-03 7.5546026E-02 at 90iterations 8.5230579E-04 3.0189514E-02 at 100iterations 3.4706286E-04 1.3288021E-02 at 110iterations 1.4466369E-04 5.4969788E-03 at 120iterations finished qdiffx linear iterations at : 16:59:53 total time elapsed so far: 10.30000 # loops : 120 mean,max change (kT/e) : 1.4466369E-04 5.4969788E-03 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.45000 DelPhi exited at 16:59:54 10.452u 0.467s 0:11.20 97.4% 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 Sat Oct 8 2011 at 16:59:54 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 = 3503 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: 2.320158 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): -4.802000 64.24500 ymin,ymax (A): 15.13700 76.70900 zmin,zma (A): -13.21900 34.74600 x,y,z range (A): 69.04700 61.57200 47.96500 scale (grids/A): 2.320158 object centre (A): 29.72150 45.92300 10.76350 number of atom coordinates read : 3503 total number of charged atoms : 3358 net assigned charge : -3.999995 assigned positive charge : 527.6923 centred at (gu) : 90.88502 77.53409 87.35817 assigned negative charge : -531.6938 centred at (gu) : 91.05505 77.82415 87.37669 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 153129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29338 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 68398 mr = 111264 m= 17076 mr = 53660 m= 2342 mr = 12394 m= 102 mr = 1455 m= 0 mr = 14 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 62260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 26788 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) : 1.546772 object centre at (A) : 29.72150 45.92300 10.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0315590E-02 -5.3500412E-03 midg,1,midg; midg,igrid,midg -0.3117166 -0.2074288 1,midg,midg; igrid,midg,midg 0.4533636 -6.5387756E-02 gauss-seidel spectral radius is 0.9990821 estimated iterations to convergence 261 setup time was (sec) 1.670000 now iterating at: 16:59:56 rms-change max change #iterations 8.568210 230.1754 at 10iterations 4.721740 114.1150 at 20iterations 2.587187 59.79427 at 30iterations 1.410405 37.79503 at 40iterations 0.7659501 16.61880 at 50iterations 0.4156033 9.967712 at 60iterations 0.2251258 4.830525 at 70iterations 0.1220735 2.408284 at 80iterations 6.5982491E-02 1.338535 at 90iterations 3.5591606E-02 0.7341180 at 100iterations 1.9229403E-02 0.3903656 at 110iterations 1.0399784E-02 0.2285461 at 120iterations 5.6030261E-03 0.1154728 at 130iterations 3.0339735E-03 6.2311172E-02 at 140iterations 1.6434073E-03 3.6060333E-02 at 150iterations 8.9329801E-04 2.1707535E-02 at 160iterations 4.9043144E-04 1.0659337E-02 at 170iterations 2.7314911E-04 6.4268112E-03 at 180iterations finished qdiffx linear iterations at : 17:00:12 total time elapsed so far: 17.31000 # loops : 180 mean,max change (kT/e) : 2.7314911E-04 6.4268112E-03 energy calculations done at 17.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.49000 DelPhi exited at 17:00:12 17.497u 0.456s 0:18.24 98.3% 0+0k 0+0io 0pf+0w