Sat Oct 8 17:00:12 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 Sat Oct 8 2011 at 17:00:12 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 !!! WARNING: ASL 224 has a net charge of -0.1000 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 : -4.099997 assigned positive charge : 533.1924 centred at (gu) : 90.20481 87.24963 89.37439 assigned negative charge : -537.2938 centred at (gu) : 90.24240 87.31661 89.37998 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 = 0.1900000 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 = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 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 -7.4072921E-11 -7.6669657E-11 midg,1,midg; midg,igrid,midg 1.7675443E-10 -1.1713713E-10 1,midg,midg; igrid,midg,midg 1.1850628E-11 -1.7585733E-10 gauss-seidel spectral radius is 0.9806618 estimated iterations to convergence 59 setup time was (sec) 0.6600000 now iterating at: 17:00:13 rms-change max change #iterations 6.1789416E-02 14.77010 at 10iterations 3.5881293E-03 0.6481552 at 20iterations 2.1720554E-04 3.4255981E-02 at 30iterations 1.7230444E-05 2.8157234E-03 at 40iterations 2.2890533E-06 4.0912628E-04 at 50iterations finished qdiffx linear iterations at : 17:00:17 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 2.2890533E-06 4.0912628E-04 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 17:00:18 4.700u 0.405s 0:05.39 94.6% 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 17:00:18 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 !!! WARNING: ASL 224 has a net charge of -0.1000 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 : -4.099997 assigned positive charge : 533.1924 centred at (gu) : 90.61371 81.74821 88.12228 assigned negative charge : -537.2938 centred at (gu) : 90.72679 81.94938 88.13944 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 = 0.2700000 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 0.6400000 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 -8.7680433E-05 -3.1624612E-04 midg,1,midg; midg,igrid,midg -1.3284801E-02 -1.0855307E-02 1,midg,midg; igrid,midg,midg 1.1262827E-02 -4.3025478E-03 gauss-seidel spectral radius is 0.9980025 estimated iterations to convergence 178 setup time was (sec) 0.8300000 now iterating at: 17:00:19 rms-change max change #iterations 3.252585 172.0320 at 10iterations 1.294501 48.88202 at 20iterations 0.5190522 19.03490 at 30iterations 0.2074253 8.722313 at 40iterations 8.2898080E-02 2.974407 at 50iterations 3.3186492E-02 1.179436 at 60iterations 1.3347649E-02 0.5010602 at 70iterations 5.3371708E-03 0.1997280 at 80iterations 2.1456426E-03 7.6545954E-02 at 90iterations 8.6651283E-04 3.1581879E-02 at 100iterations 3.5458271E-04 1.3619900E-02 at 110iterations 1.4922091E-04 5.6648254E-03 at 120iterations finished qdiffx linear iterations at : 17:00:29 total time elapsed so far: 10.58000 # loops : 120 mean,max change (kT/e) : 1.4922091E-04 5.6648254E-03 energy calculations done at 10.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.75000 DelPhi exited at 17:00:29 10.750u 0.444s 0:11.50 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 Sat Oct 8 2011 at 17:00:29 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 !!! WARNING: ASL 224 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 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 : -4.099997 assigned positive charge : 533.1924 centred at (gu) : 90.92017 77.62203 87.18309 assigned negative charge : -537.2938 centred at (gu) : 91.09021 77.92403 87.20914 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 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 1.370000 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 1.550000 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 1.5468496E-02 -5.9139193E-03 midg,1,midg; midg,igrid,midg -0.3071895 -0.2102998 1,midg,midg; igrid,midg,midg 0.4502361 -7.0752993E-02 gauss-seidel spectral radius is 0.9990821 estimated iterations to convergence 261 setup time was (sec) 1.750000 now iterating at: 17:00:31 rms-change max change #iterations 8.676968 230.1752 at 10iterations 4.777499 114.1149 at 20iterations 2.617701 61.38934 at 30iterations 1.426256 38.06194 at 40iterations 0.7744405 16.50823 at 50iterations 0.4200286 10.18760 at 60iterations 0.2275313 4.685261 at 70iterations 0.1233353 2.429863 at 80iterations 6.6664159E-02 1.330042 at 90iterations 3.5952050E-02 0.7342286 at 100iterations 1.9415515E-02 0.4027710 at 110iterations 1.0498364E-02 0.2295685 at 120iterations 5.6535136E-03 0.1178207 at 130iterations 3.0575900E-03 6.2229156E-02 at 140iterations 1.6523576E-03 3.7326813E-02 at 150iterations 8.9437247E-04 2.0935059E-02 at 160iterations 4.8696314E-04 1.0874987E-02 at 170iterations 2.6720107E-04 6.0625076E-03 at 180iterations finished qdiffx linear iterations at : 17:00:47 total time elapsed so far: 17.69000 # loops : 180 mean,max change (kT/e) : 2.6720107E-04 6.0625076E-03 energy calculations done at 17.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.86000 DelPhi exited at 17:00:48 17.868u 0.446s 0:18.61 98.3% 0+0k 0+0io 0pf+0w