Sat Oct 8 19:35:00 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 19:35:00 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 366 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6268047 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): -32.04100 17.50200 ymin,ymax (A): -23.08800 23.28800 zmin,zma (A): -12.36800 44.42800 x,y,z range (A): 49.54300 46.37600 56.79600 scale (grids/A): 0.6268047 object centre (A): -7.269500 0.1000004 16.03000 number of atom coordinates read : 2586 total number of charged atoms : 2462 net assigned charge : 5.000007 assigned positive charge : 394.9380 centred at (gu) : 88.63763 89.00069 89.90256 assigned negative charge : -389.9385 centred at (gu) : 88.54084 89.02678 89.78191 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6698 nv = 96 ne = 84 npr = 53431 no. pairs analyzed = 53431 no. exposed pairs = 3047 no. arc points = 21752 no. surface atoms = 1017 nbur = 1569 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3775 m= 4 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.2000000 number of dielectric boundary points 3219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2123 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8159 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9622821E-09 1.4375434E-08 midg,1,midg; midg,igrid,midg 8.8730863E-09 2.3964153E-09 1,midg,midg; igrid,midg,midg -4.0078487E-09 9.5365751E-09 gauss-seidel spectral radius is 0.9868118 estimated iterations to convergence 71 setup time was (sec) 0.4500000 now iterating at: 19:35:00 rms-change max change #iterations 0.1374923 21.00533 at 10iterations 1.3031811E-02 1.969833 at 20iterations 1.2819750E-03 0.1767883 at 30iterations 1.2120778E-04 1.7395020E-02 at 40iterations 1.4239901E-05 2.2106171E-03 at 50iterations finished qdiffx linear iterations at : 19:35:04 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.4239901E-05 2.2106171E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 19:35:04 4.310u 0.279s 0:04.85 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 19:35:05 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 366 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.880414 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): -32.04100 17.50200 ymin,ymax (A): -23.08800 23.28800 zmin,zma (A): -12.36800 44.42800 x,y,z range (A): 49.54300 46.37600 56.79600 scale (grids/A): 1.880414 object centre (A): -7.269500 0.1000004 16.03000 number of atom coordinates read : 2586 total number of charged atoms : 2462 net assigned charge : 5.000007 assigned positive charge : 394.9380 centred at (gu) : 85.91247 87.00171 89.70712 assigned negative charge : -389.9385 centred at (gu) : 85.62226 87.07992 89.34526 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21752 grid for indexing accessible points = 1.400000 m= 26286 mr = 50817 m= 3930 mr = 19689 m= 198 mr = 2521 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4438 time to turn everything in is 0.3900000 number of dielectric boundary points 29709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 19332 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) : 0.6268047 object centre at (A) : -7.269500 0.1000004 16.03000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6006256E-02 2.4688857E-02 midg,1,midg; midg,igrid,midg 1.2355149E-02 3.3386215E-03 1,midg,midg; igrid,midg,midg -5.0211525E-05 3.7333060E-02 gauss-seidel spectral radius is 0.9985946 estimated iterations to convergence 211 setup time was (sec) 0.7000000 now iterating at: 19:35:06 rms-change max change #iterations 4.173062 245.4924 at 10iterations 1.927104 71.56133 at 20iterations 0.8941737 29.67052 at 30iterations 0.4132211 14.84128 at 40iterations 0.1917571 6.315220 at 50iterations 8.9081571E-02 2.996216 at 60iterations 4.1313175E-02 1.357222 at 70iterations 1.9139078E-02 0.6064079 at 80iterations 8.8813752E-03 0.2966738 at 90iterations 4.1122921E-03 0.1361904 at 100iterations 1.9029304E-03 5.9777260E-02 at 110iterations 8.8206684E-04 2.9689789E-02 at 120iterations finished qdiffx linear iterations at : 19:35:15 total time elapsed so far: 10.12000 # loops : 120 mean,max change (kT/e) : 8.8206684E-04 2.9689789E-02 energy calculations done at 10.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.25000 DelPhi exited at 19:35:15 10.255u 0.338s 0:10.89 97.1% 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 19:35:15 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 366 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.820621 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): -32.04100 17.50200 ymin,ymax (A): -23.08800 23.28800 zmin,zma (A): -12.36800 44.42800 x,y,z range (A): 49.54300 46.37600 56.79600 scale (grids/A): 2.820621 object centre (A): -7.269500 0.1000004 16.03000 number of atom coordinates read : 2586 total number of charged atoms : 2462 net assigned charge : 5.000007 assigned positive charge : 394.9380 centred at (gu) : 83.86845 85.50233 89.56054 assigned negative charge : -389.9385 centred at (gu) : 83.43335 85.61981 89.01791 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 167251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21752 grid for indexing accessible points = 1.400000 m= 85632 mr = 122661 m= 30594 mr = 70927 m= 7068 mr = 24808 m= 885 mr = 5369 m= 29 mr = 561 m= 0 mr = 6 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 15704 time to turn everything in is 1.020000 number of dielectric boundary points 67127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 19696 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) : 1.880414 object centre at (A) : -7.269500 0.1000004 16.03000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0123045E-02 0.2731856 midg,1,midg; midg,igrid,midg 0.1531165 2.8580802E-02 1,midg,midg; igrid,midg,midg 1.2978623E-02 0.4512869 gauss-seidel spectral radius is 0.9992426 estimated iterations to convergence 287 setup time was (sec) 1.360000 now iterating at: 19:35:17 rms-change max change #iterations 9.748575 330.9225 at 10iterations 5.609766 131.9430 at 20iterations 3.227584 69.36089 at 30iterations 1.845116 39.92578 at 40iterations 1.058640 21.16309 at 50iterations 0.6041292 13.35068 at 60iterations 0.3462342 6.569618 at 70iterations 0.1978837 4.470359 at 80iterations 0.1130139 2.390884 at 90iterations 6.4608037E-02 1.236097 at 100iterations 3.6804881E-02 0.6783447 at 110iterations 2.0987974E-02 0.3815379 at 120iterations 1.2018536E-02 0.2396243 at 130iterations 6.8493951E-03 0.1184406 at 140iterations 3.9062719E-03 7.1895599E-02 at 150iterations 2.2250556E-03 3.8993835E-02 at 160iterations 1.2689454E-03 2.2722244E-02 at 170iterations 7.2496413E-04 1.5068054E-02 at 180iterations finished qdiffx linear iterations at : 19:35:33 total time elapsed so far: 16.73000 # loops : 180 mean,max change (kT/e) : 7.2496413E-04 1.5068054E-02 energy calculations done at 16.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.86000 DelPhi exited at 19:35:33 16.862u 0.365s 0:17.69 97.3% 0+0k 0+0io 0pf+0w