Tue Oct 11 07:08:25 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 Tue Oct 11 2011 at 07:08:25 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 !!! WARNING: UMP 1145 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4605910 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): -70.91700 5.995000 ymin,ymax (A): -83.91800 -30.35000 zmin,zma (A): -54.11900 23.17300 x,y,z range (A): 76.91200 53.56800 77.29200 scale (grids/A): 0.4605910 object centre (A): -32.46100 -57.13400 -15.47300 number of atom coordinates read : 3398 total number of charged atoms : 3193 net assigned charge : 1.900010 assigned positive charge : 506.2044 centred at (gu) : 84.88797 89.97763 96.30289 assigned negative charge : -504.3059 centred at (gu) : 84.77310 90.04259 96.35938 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4506 nv = 96 ne = 84 npr = 67032 no. pairs analyzed = 67032 no. exposed pairs = 4331 no. arc points = 30153 no. surface atoms = 1474 nbur = 1924 mkacc time = 0.1500000 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 = 1.848000 m= 129 mr = 2240 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2640 ## 515 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6011 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0969595E-12 -3.5506487E-11 midg,1,midg; midg,igrid,midg 1.3661919E-11 -6.3152886E-12 1,midg,midg; igrid,midg,midg -6.7423359E-11 4.9455748E-12 gauss-seidel spectral radius is 0.9758389 estimated iterations to convergence 53 setup time was (sec) 0.6000000 now iterating at: 07:08:26 rms-change max change #iterations 3.2676473E-02 6.892015 at 10iterations 2.2200623E-03 0.3845100 at 20iterations 6.3015631E-04 0.1390631 at 30iterations 2.3384794E-04 5.2937984E-02 at 40iterations 8.7843961E-05 2.0051003E-02 at 50iterations finished qdiffx linear iterations at : 07:08:28 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 8.7843961E-05 2.0051003E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 07:08:29 3.506u 0.208s 0:04.04 91.5% 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 Tue Oct 11 2011 at 07:08:29 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 !!! WARNING: UMP 1145 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.381773 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): -70.91700 5.995000 ymin,ymax (A): -83.91800 -30.35000 zmin,zma (A): -54.11900 23.17300 x,y,z range (A): 76.91200 53.56800 77.29200 scale (grids/A): 1.381773 object centre (A): -32.46100 -57.13400 -15.47300 number of atom coordinates read : 3398 total number of charged atoms : 3193 net assigned charge : 1.900010 assigned positive charge : 506.2044 centred at (gu) : 74.66263 89.93204 108.9074 assigned negative charge : -504.3059 centred at (gu) : 74.31886 90.12740 109.0781 start vw surface at 0.1600000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 51261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30153 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 14472 mr = 34083 m= 948 mr = 9855 m= 13 mr = 397 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 22359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 492 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 22998 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) : 0.4605910 object centre at (A) : -32.46100 -57.13400 -15.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5909212E-05 -7.2090363E-05 midg,1,midg; midg,igrid,midg 3.1460640E-03 8.3606609E-04 1,midg,midg; igrid,midg,midg 3.7221191E-03 -5.8813894E-05 gauss-seidel spectral radius is 0.9974005 estimated iterations to convergence 156 setup time was (sec) 0.7000000 now iterating at: 07:08:30 rms-change max change #iterations 2.378365 130.8234 at 10iterations 0.8317510 42.09181 at 20iterations 0.2923369 12.70894 at 30iterations 0.1032166 4.810608 at 40iterations 3.6318403E-02 1.552094 at 50iterations 1.3042934E-02 0.5814233 at 60iterations 4.9545211E-03 0.2081928 at 70iterations 2.1609671E-03 0.1075993 at 80iterations 1.1990619E-03 5.5519104E-02 at 90iterations 7.9606374E-04 3.7523746E-02 at 100iterations 5.6462927E-04 2.5637150E-02 at 110iterations 4.0719140E-04 1.8416405E-02 at 120iterations finished qdiffx linear iterations at : 07:08:36 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 4.0719140E-04 1.8416405E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 07:08:37 7.486u 0.268s 0:08.18 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 Tue Oct 11 2011 at 07:08:37 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 !!! WARNING: UMP 1145 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: 2.072659 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): -70.91700 5.995000 ymin,ymax (A): -83.91800 -30.35000 zmin,zma (A): -54.11900 23.17300 x,y,z range (A): 76.91200 53.56800 77.29200 scale (grids/A): 2.072659 object centre (A): -32.46100 -57.13400 -15.47300 number of atom coordinates read : 3398 total number of charged atoms : 3193 net assigned charge : 1.900010 assigned positive charge : 506.2044 centred at (gu) : 66.99364 89.89768 118.3608 assigned negative charge : -504.3059 centred at (gu) : 66.47820 90.19089 118.6170 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 119449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30153 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 52296 mr = 83763 m= 12474 mr = 40978 m= 1307 mr = 9379 m= 29 mr = 762 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 50673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 25321 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) : 1.381773 object centre at (A) : -32.46100 -57.13400 -15.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6212750E-03 0.1921855 midg,1,midg; midg,igrid,midg 6.0112871E-02 1.9318013E-02 1,midg,midg; igrid,midg,midg 8.3278574E-02 -2.0528627E-03 gauss-seidel spectral radius is 0.9988161 estimated iterations to convergence 230 setup time was (sec) 1.230000 now iterating at: 07:08:39 rms-change max change #iterations 6.852981 225.0705 at 10iterations 3.505554 112.7929 at 20iterations 1.776706 51.45338 at 30iterations 0.8959340 29.03679 at 40iterations 0.4500968 12.11608 at 50iterations 0.2252670 6.464888 at 60iterations 0.1127409 2.974052 at 70iterations 5.6236602E-02 1.377207 at 80iterations 2.8116798E-02 0.7195492 at 90iterations 1.4275941E-02 0.3741436 at 100iterations 7.4419389E-03 0.2070694 at 110iterations 4.0772445E-03 0.1175804 at 120iterations 2.4692582E-03 7.7228546E-02 at 130iterations 1.6778461E-03 4.7958374E-02 at 140iterations 1.2512216E-03 3.4295559E-02 at 150iterations 9.8251051E-04 2.5178909E-02 at 160iterations 7.8716851E-04 1.9830465E-02 at 170iterations 6.3633936E-04 1.6044617E-02 at 180iterations finished qdiffx linear iterations at : 07:08:49 total time elapsed so far: 11.63000 # loops : 180 mean,max change (kT/e) : 6.3633936E-04 1.6044617E-02 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 07:08:50 11.810u 0.262s 0:12.57 96.0% 0+0k 0+0io 0pf+0w