Sun Oct 9 16:42:14 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 16:42:14 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2995 !!! WARNING: ASL 39 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5196852 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): 23.84600 81.42900 ymin,ymax (A): -24.43200 26.78300 zmin,zma (A): -37.91900 30.58400 x,y,z range (A): 57.58300 51.21500 68.50301 scale (grids/A): 0.5196852 object centre (A): 52.63750 1.175500 -3.667501 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : -1.099994 assigned positive charge : 449.0578 centred at (gu) : 90.20282 88.74403 90.90648 assigned negative charge : -450.1595 centred at (gu) : 90.24525 88.81730 90.86775 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5088 nv = 96 ne = 84 npr = 59912 no. pairs analyzed = 59912 no. exposed pairs = 4190 no. arc points = 29450 no. surface atoms = 1391 nbur = 1604 mkacc time = 0.1300000 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 = 1.624000 m= 187 mr = 2301 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2931 ## 438 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4289111E-11 8.3948050E-11 midg,1,midg; midg,igrid,midg 2.0580589E-10 -1.4649121E-10 1,midg,midg; igrid,midg,midg 7.0625464E-11 -1.3527134E-10 gauss-seidel spectral radius is 0.9809380 estimated iterations to convergence 60 setup time was (sec) 0.5400000 now iterating at: 16:42:15 rms-change max change #iterations 5.8394462E-02 11.74662 at 10iterations 3.4720947E-03 0.5544825 at 20iterations 2.5857292E-04 4.5047760E-02 at 30iterations 5.0555143E-05 1.0573864E-02 at 40iterations 1.4608619E-05 3.1280518E-03 at 50iterations finished qdiffx linear iterations at : 16:42:17 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.4608619E-05 3.1280518E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 16:42:18 3.103u 0.129s 0:03.53 91.2% 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 16:42:18 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2995 !!! WARNING: ASL 39 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.559056 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): 23.84600 81.42900 ymin,ymax (A): -24.43200 26.78300 zmin,zma (A): -37.91900 30.58400 x,y,z range (A): 57.58300 51.21500 68.50301 scale (grids/A): 1.559056 object centre (A): 52.63750 1.175500 -3.667501 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : -1.099994 assigned positive charge : 449.0578 centred at (gu) : 90.60778 86.23077 92.71881 assigned negative charge : -450.1595 centred at (gu) : 90.73509 86.45184 92.60337 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 56312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 16128 mr = 35497 m= 1655 mr = 10169 m= 35 mr = 707 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 255 time to turn everything in is 0.4200000 number of dielectric boundary points 27758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 405 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 21524 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) : 0.5196852 object centre at (A) : 52.63750 1.175500 -3.667501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0213383E-02 -5.6324364E-04 midg,1,midg; midg,igrid,midg 4.4761943E-03 -5.0350097E-03 1,midg,midg; igrid,midg,midg -1.3869401E-03 -1.0490753E-03 gauss-seidel spectral radius is 0.9980114 estimated iterations to convergence 178 setup time was (sec) 0.6900000 now iterating at: 16:42:18 rms-change max change #iterations 3.049119 140.2212 at 10iterations 1.217610 51.59026 at 20iterations 0.4850124 19.11637 at 30iterations 0.1930579 7.441175 at 40iterations 7.7719204E-02 3.089893 at 50iterations 3.1078061E-02 1.277815 at 60iterations 1.2344183E-02 0.4777832 at 70iterations 4.9789804E-03 0.1919460 at 80iterations 2.0084530E-03 8.0160141E-02 at 90iterations 8.1402651E-04 3.3470154E-02 at 100iterations 3.3571210E-04 1.3750076E-02 at 110iterations 1.4595786E-04 5.7468414E-03 at 120iterations finished qdiffx linear iterations at : 16:42:24 total time elapsed so far: 6.660000 # loops : 120 mean,max change (kT/e) : 1.4595786E-04 5.7468414E-03 energy calculations done at 6.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.830000 DelPhi exited at 16:42:25 6.832u 0.158s 0:07.30 95.6% 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 Sun Oct 9 2011 at 16:42:25 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2995 !!! WARNING: ASL 39 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: 2.338583 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): 23.84600 81.42900 ymin,ymax (A): -24.43200 26.78300 zmin,zma (A): -37.91900 30.58400 x,y,z range (A): 57.58300 51.21500 68.50301 scale (grids/A): 2.338583 object centre (A): 52.63750 1.175500 -3.667501 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : -1.099994 assigned positive charge : 449.0578 centred at (gu) : 90.91123 84.34592 94.07820 assigned negative charge : -450.1595 centred at (gu) : 91.10265 84.67768 93.90499 start vw surface at 0.1600000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 130819 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 55584 mr = 87972 m= 15543 mr = 41350 m= 2374 mr = 11035 m= 131 mr = 1431 m= 5 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 694 time to turn everything in is 0.9600000 number of dielectric boundary points 62644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 22747 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) : 1.559056 object centre at (A) : 52.63750 1.175500 -3.667501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4195674 2.0299129E-02 midg,1,midg; midg,igrid,midg 0.1098917 -8.6769290E-02 1,midg,midg; igrid,midg,midg -5.3529125E-02 -3.1452030E-03 gauss-seidel spectral radius is 0.9990861 estimated iterations to convergence 261 setup time was (sec) 1.240000 now iterating at: 16:42:26 rms-change max change #iterations 8.197115 283.1399 at 10iterations 4.558231 118.5946 at 20iterations 2.512802 64.35225 at 30iterations 1.381536 37.25262 at 40iterations 0.7556701 17.85047 at 50iterations 0.4122467 9.952140 at 60iterations 0.2244389 6.725050 at 70iterations 0.1220135 3.063506 at 80iterations 6.6143923E-02 1.659995 at 90iterations 3.5769459E-02 0.7995988 at 100iterations 1.9425547E-02 0.5113983 at 110iterations 1.0486426E-02 0.2329099 at 120iterations 5.6884740E-03 0.1369495 at 130iterations 3.0650273E-03 6.4489365E-02 at 140iterations 1.6583671E-03 3.7311554E-02 at 150iterations 8.9644990E-04 1.9484520E-02 at 160iterations 4.8304384E-04 1.0504723E-02 at 170iterations 2.6102256E-04 5.5770874E-03 at 180iterations finished qdiffx linear iterations at : 16:42:36 total time elapsed so far: 10.64000 # loops : 180 mean,max change (kT/e) : 2.6102256E-04 5.5770874E-03 energy calculations done at 10.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 16:42:36 10.807u 0.163s 0:11.30 96.9% 0+0k 0+0io 0pf+0w