Sat Oct 15 14:45:16 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 15 2011 at 14:45:17 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 = 3026 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 0.5471956 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): -47.66100 17.39800 ymin,ymax (A): -17.93400 27.60100 zmin,zma (A): -43.10300 4.777000 x,y,z range (A): 65.05901 45.53500 47.88000 scale (grids/A): 0.5471956 object centre (A): -15.13150 4.833500 -19.16300 number of atom coordinates read : 3026 total number of charged atoms : 2885 net assigned charge : -0.4999879 assigned positive charge : 454.1829 centred at (gu) : 90.48608 90.10159 89.62045 assigned negative charge : -454.6841 centred at (gu) : 90.54492 90.19605 89.53094 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5886 nv = 96 ne = 84 npr = 60411 no. pairs analyzed = 60411 no. exposed pairs = 3957 no. arc points = 27914 no. surface atoms = 1342 nbur = 1684 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= 216 mr = 2913 m= 0 mr = 6 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2852 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7686 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3732209E-10 5.4867039E-10 midg,1,midg; midg,igrid,midg 6.2183575E-10 -7.2444806E-10 1,midg,midg; igrid,midg,midg 3.4454514E-10 -5.0604765E-10 gauss-seidel spectral radius is 0.9827878 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 14:45:18 rms-change max change #iterations 7.3476851E-02 12.66183 at 10iterations 4.8237955E-03 0.9034100 at 20iterations 3.2473041E-04 5.4534912E-02 at 30iterations 2.1493555E-05 3.8442612E-03 at 40iterations 1.4968170E-06 2.5367737E-04 at 50iterations finished qdiffx linear iterations at : 14:45:23 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 1.4968170E-06 2.5367737E-04 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:45:23 3.761u 0.240s 0:06.04 66.2% 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 Sat Oct 15 2011 at 14:45:24 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 = 3026 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 1.641587 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): -47.66100 17.39800 ymin,ymax (A): -17.93400 27.60100 zmin,zma (A): -43.10300 4.777000 x,y,z range (A): 65.05901 45.53500 47.88000 scale (grids/A): 1.641587 object centre (A): -15.13150 4.833500 -19.16300 number of atom coordinates read : 3026 total number of charged atoms : 2885 net assigned charge : -0.4999879 assigned positive charge : 454.1829 centred at (gu) : 91.45752 90.30411 88.86056 assigned negative charge : -454.6841 centred at (gu) : 91.63442 90.58772 88.59261 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27914 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19159 mr = 43504 m= 1719 mr = 12601 m= 42 mr = 725 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.3200000 number of dielectric boundary points 29593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 321 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 22116 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) : 0.5471956 object centre at (A) : -15.13150 4.833500 -19.16300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4234696E-02 4.3293796E-03 midg,1,midg; midg,igrid,midg 4.8338417E-03 -3.0878086E-03 1,midg,midg; igrid,midg,midg 4.5797872E-04 -1.9562621E-02 gauss-seidel spectral radius is 0.9982114 estimated iterations to convergence 188 setup time was (sec) 0.5600000 now iterating at: 14:45:24 rms-change max change #iterations 3.377130 157.2751 at 10iterations 1.409234 55.54999 at 20iterations 0.5905198 22.00905 at 30iterations 0.2471801 10.66271 at 40iterations 0.1029427 3.755211 at 50iterations 4.3337919E-02 1.859818 at 60iterations 1.8156322E-02 0.6291466 at 70iterations 7.5999410E-03 0.2630326 at 80iterations 3.1973305E-03 0.1085815 at 90iterations 1.3409114E-03 4.6245575E-02 at 100iterations 5.6168099E-04 1.8793106E-02 at 110iterations 2.3510336E-04 8.7952614E-03 at 120iterations finished qdiffx linear iterations at : 14:45:42 total time elapsed so far: 8.630000 # loops : 120 mean,max change (kT/e) : 2.3510336E-04 8.7952614E-03 energy calculations done at 8.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.760000 DelPhi exited at 14:45:43 8.758u 0.278s 0:19.35 46.6% 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 15 2011 at 14:45:43 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 = 3026 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 2.462380 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): -47.66100 17.39800 ymin,ymax (A): -17.93400 27.60100 zmin,zma (A): -43.10300 4.777000 x,y,z range (A): 65.05901 45.53500 47.88000 scale (grids/A): 2.462380 object centre (A): -15.13150 4.833500 -19.16300 number of atom coordinates read : 3026 total number of charged atoms : 2885 net assigned charge : -0.4999879 assigned positive charge : 454.1829 centred at (gu) : 92.18610 90.45591 88.29058 assigned negative charge : -454.6841 centred at (gu) : 92.45164 90.88165 87.88877 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27914 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67551 mr = 106703 m= 17868 mr = 52394 m= 2537 mr = 12766 m= 142 mr = 1517 m= 0 mr = 48 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 905 time to turn everything in is 0.7900000 number of dielectric boundary points 66771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 23049 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) : 1.641587 object centre at (A) : -15.13150 4.833500 -19.16300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2090204 7.9208434E-02 midg,1,midg; midg,igrid,midg 6.7336373E-02 -3.8162816E-02 1,midg,midg; igrid,midg,midg 5.9295602E-02 -0.7783603 gauss-seidel spectral radius is 0.9991513 estimated iterations to convergence 271 setup time was (sec) 1.050000 now iterating at: 14:45:45 rms-change max change #iterations 8.823588 273.1465 at 10iterations 4.962879 119.7679 at 20iterations 2.777542 71.26279 at 30iterations 1.547037 38.63971 at 40iterations 0.8597502 18.47900 at 50iterations 0.4757865 11.19739 at 60iterations 0.2630806 5.231868 at 70iterations 0.1455634 2.969028 at 80iterations 8.0637805E-02 1.748829 at 90iterations 4.4400103E-02 0.8816299 at 100iterations 2.4573453E-02 0.5191202 at 110iterations 1.3543551E-02 0.2855225 at 120iterations 7.4760714E-03 0.1511989 at 130iterations 4.1202167E-03 0.1027317 at 140iterations 2.2729565E-03 4.8358917E-02 at 150iterations 1.2511569E-03 2.4206161E-02 at 160iterations 6.9015170E-04 1.6109467E-02 at 170iterations 3.8062560E-04 7.8811646E-03 at 180iterations finished qdiffx linear iterations at : 14:45:59 total time elapsed so far: 13.84000 # loops : 180 mean,max change (kT/e) : 3.8062560E-04 7.8811646E-03 energy calculations done at 13.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.98000 DelPhi exited at 14:45:59 13.980u 0.298s 0:16.09 88.6% 0+0k 0+0io 0pf+0w